Revision: 18392
http://sourceforge.net/p/jmol/code/18392
Author: hansonr
Date: 2013-07-01 18:38:26 +0000 (Mon, 01 Jul 2013)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagResReader.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/util/Matrix3f.java
trunk/Jmol/src/org/jmol/util/Quaternion.java
trunk/Jmol/src/org/jmol/util/Tensor.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagResReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagResReader.java
2013-07-01 15:45:20 UTC (rev 18391)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagResReader.java
2013-07-01 18:38:26 UTC (rev 18392)
@@ -86,11 +86,9 @@
private void readTensorNew() throws Exception {
String[] tokens = getTokens();
String id = tokens[0];
- int pt = id.indexOf("_");
- String type = (pt < 0 ? id : id.substring(0, pt));
String atomName1 = getAtomName(tokens[1], tokens[2]);
- pt = 3;
- String atomName2 = (type.equals("isc") ? getAtomName(tokens[pt++],
tokens[pt++]) : null);
+ int pt = 3;
+ String atomName2 = (id.startsWith("isc") ? getAtomName(tokens[pt++],
tokens[pt++]) : null);
// TODO: maxIso for isc?
double[][] a = new double[3][3];
for (int i = 0; i < 3; i++)
@@ -98,7 +96,7 @@
a[i][j] = Double.valueOf(tokens[pt++]).doubleValue();
int index1 = atomSetCollection.getAtomIndexFromName(atomName1);
int index2;
- Tensor t = Tensor.getTensorFromAsymmetricTensor(a, type);
+ Tensor t = Tensor.getTensorFromAsymmetricTensor(a, id);
if (atomName2 == null) {
index2 = -1;
atomSetCollection.getAtoms()[index1].addTensor(t, null);
@@ -106,12 +104,13 @@
} else {
index2 = atomSetCollection.getAtomIndexFromName(atomName2);
}
- t.setAtomIndexes(index1, index2);
- if (tensorTypes.indexOf(type) < 0) {
- tensorTypes += type;
- appendLoadNote("Ellipsoids set \"" + type + "\": "
- + (type.equals("ms") ? "Magnetic Shielding" :
- type.equals("efg") ? "Electric Field Gradient" :
type.equals("isc") ? "Coupling" : "?"));
+ t.setAtomIndexes(index1, index2);
+ String key = ";" + id +";";
+ if (tensorTypes.indexOf(key) < 0) {
+ tensorTypes += key;
+ appendLoadNote("Ellipsoids set \"" + id + "\": "
+ + (id.startsWith("ms") ? "Magnetic Shielding" :
+ id.startsWith("efg") ? "Electric Field Gradient" :
id.startsWith("isc") ? "J-Coupling" : "?"));
}
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-01
15:45:20 UTC (rev 18391)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-01
18:38:26 UTC (rev 18392)
@@ -3374,6 +3374,7 @@
// q%-5 Matrix column 2
// q%-6 AxisAngle format
// q%-9 Matrix format
+ // q%-10 EulerZXZ (degrees)
case 0:
return addXFloat(pt4.w);
case 1:
@@ -3382,24 +3383,31 @@
return addXFloat(pt4.y);
case 3:
return addXFloat(pt4.z);
+ }
+ Quaternion q = Quaternion.newP4(pt4);
+ switch(n) {
case 4:
- return addXPt(P3.newP((Quaternion.newP4(pt4)).getNormal()));
+ return addXPt(P3.newP(q.getNormal()));
+ case 5:
+ return addXAF(q.getEulerZXZ());
+ case 6:
+ return addXAF(q.getEulerZXZ());
case -1:
- return addXPt(P3.newP(Quaternion.newP4(pt4).getVector(-1)));
+ return addXPt(P3.newP(q.getVector(-1)));
case -2:
- return addXFloat((Quaternion.newP4(pt4)).getTheta());
+ return addXFloat(q.getTheta());
case -3:
- return addXPt(P3.newP((Quaternion.newP4(pt4)).getVector(0)));
+ return addXPt(P3.newP(q.getVector(0)));
case -4:
- return addXPt(P3.newP((Quaternion.newP4(pt4)).getVector(1)));
+ return addXPt(P3.newP(q.getVector(1)));
case -5:
- return addXPt(P3.newP((Quaternion.newP4(pt4)).getVector(2)));
+ return addXPt(P3.newP(q.getVector(2)));
case -6:
- AxisAngle4f ax = (Quaternion.newP4(pt4)).toAxisAngle4f();
+ AxisAngle4f ax = q.toAxisAngle4f();
return addXPt4(P4.new4(ax.x, ax.y, ax.z,
(float) (ax.angle * 180 / Math.PI)));
case -9:
- return addXM3((Quaternion.newP4(pt4)).getMatrix());
+ return addXM3(q.getMatrix());
default:
return addXPt4(pt4);
}
Modified: trunk/Jmol/src/org/jmol/util/Matrix3f.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Matrix3f.java 2013-07-01 15:45:20 UTC (rev
18391)
+++ trunk/Jmol/src/org/jmol/util/Matrix3f.java 2013-07-01 18:38:26 UTC (rev
18392)
@@ -28,6 +28,8 @@
* additions by Bob Hanson [email protected] 9/30/2012 for unique
* constructor and method names for the optimization of compiled
* JavaScript using Java2Script
+ *
+ *
*/
public class Matrix3f implements Serializable {
Modified: trunk/Jmol/src/org/jmol/util/Quaternion.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Quaternion.java 2013-07-01 15:45:20 UTC
(rev 18391)
+++ trunk/Jmol/src/org/jmol/util/Quaternion.java 2013-07-01 18:38:26 UTC
(rev 18392)
@@ -48,6 +48,7 @@
private Matrix3f mat;
private final static P4 qZero = new P4();
+ private static final double RAD_PER_DEG = Math.PI / 180;
public Quaternion() {
q0 = 1;
@@ -136,9 +137,9 @@
q0 = 1;
return;
}
- double fact = (Math.sin(theta / 2 * Math.PI / 180) / Math.sqrt(pt.x
+ double fact = (Math.sin(theta / 2 * RAD_PER_DEG) / Math.sqrt(pt.x
* pt.x + pt.y * pt.y + pt.z * pt.z));
- q0 = (float) (Math.cos(theta / 2 * Math.PI / 180));
+ q0 = (float) (Math.cos(theta / 2 * RAD_PER_DEG));
q1 = (float) (pt.x * fact);
q2 = (float) (pt.y * fact);
q3 = (float) (pt.z * fact);
@@ -314,10 +315,10 @@
q3 *= -1;
}
- public static final Quaternion getQuaternionFrame(P3 center, Tuple3f x,
Tuple3f xy) {
+ public static final Quaternion getQuaternionFrame(P3 center, Tuple3f x,
Tuple3f y) {
V3 vA = V3.newV(x);
vA.sub(center);
- V3 vB = V3.newV(xy);
+ V3 vB = V3.newV(y);
vB.sub(center);
return getQuaternionFrameV(vA, vB, null, false);
}
@@ -802,4 +803,19 @@
return (float) Math.sqrt(sum2 / (n - 1));
}
+ public float[] getEulerZYZ() {
+ return null;
+ }
+
+ public float[] getEulerZXZ() {
+ // NOT
http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles
+ // http://www.swarthmore.edu/NatSci/mzucker1/e27/diebel2006attitude.pdf
+ double rA, rB, rG;
+ rG = Math.atan2( 2 * (q1 * q3 - q0 * q2), 2 * (q2 * q3 + q0 * q1));
+ rB = Math.acos(q3 * q3 - q2 * q2 - q1 * q1 + q0 * q0);
+ rA = Math.atan2(2 * (q1 * q3 + q0 * q2), 2 * (q0 * q1 - q2 * q3 ));
+ return new float[] {(float) (rA / RAD_PER_DEG), (float) (rB /
RAD_PER_DEG), (float) (rG / RAD_PER_DEG)};
+ }
+
+
}
Modified: trunk/Jmol/src/org/jmol/util/Tensor.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Tensor.java 2013-07-01 15:45:20 UTC (rev
18391)
+++ trunk/Jmol/src/org/jmol/util/Tensor.java 2013-07-01 18:38:26 UTC (rev
18392)
@@ -65,7 +65,10 @@
private static final String KNOWN_TYPES =
";iso....;adp....;tls-u..;tls-r..;ms.....;efg....;isc....;charge.;";
private static int getType(String type) {
- int pt = KNOWN_TYPES.indexOf(";" + type.toLowerCase() + ".");
+ int pt = type.indexOf("_");
+ if (pt >= 0)
+ type = type.substring(0, pt);
+ pt = KNOWN_TYPES.indexOf(";" + type.toLowerCase() + ".");
return (pt < 0 ? TYPE_OTHER : pt / 8);
}
@@ -110,9 +113,8 @@
public int atomIndex2 = -1;
/**
- * returns an object of the specified type, including
- * "eigenvalues", "eigenvectors", "asymmetric",
- * "symmetric", "trace", "indices", and "type"
+ * returns an object of the specified type, including "eigenvalues",
+ * "eigenvectors", "asymmetric", "symmetric", "trace", "indices", and "type"
*
* @param infoType
* @return Object or null
@@ -120,18 +122,10 @@
public Object getInfo(String infoType) {
if (infoType.charAt(0) != ';')
infoType = ";" + infoType + ".";
- switch ((";............."
- + ";eigenvalues.."
- + ";eigenvectors."
- + ";asymmetric..."
- + ";symmetric...."
- + ";trace........"
- + ";haeberlen...."
- + ";eulerzyz....."
- + ";eulerzxz....."
- + ";indices......"
- + ";type........."
- ).indexOf(infoType) / 14) {
+ switch ((";............." + ";eigenvalues.." + ";eigenvectors."
+ + ";asymmetric..." + ";symmetric...." + ";trace........"
+ + ";haeberlen...." + ";eulerzyz....." + ";eulerzxz....."
+ + ";indices......" + ";type.........").indexOf(infoType) / 14) {
case 1:
return eigenValues;
case 2:
@@ -159,25 +153,23 @@
return Float.valueOf(eigenValues[0] + eigenValues[1] + eigenValues[2]);
case 6: // haeberlen
float[] haeb = new float[3];
- haeb[0] = ((eigenValues[0] + eigenValues[1] + eigenValues[2])/3.0f);
- haeb[1] = (eigenValues[2] - (eigenValues[0]+eigenValues[1])/2.0f);
- if (haeb[1] != 0.0f)
- haeb[2] = ((eigenValues[1]-eigenValues[0])/(eigenValues[2]-haeb[0]));
- else
- haeb[2] = 0.0f;
+ haeb[0] = (eigenValues[0] + eigenValues[1] + eigenValues[2]) / 3;
+ haeb[1] = eigenValues[2] - (eigenValues[0] + eigenValues[1]) / 2;
+ haeb[2] = (haeb[1] == 0 ? 0 : (eigenValues[1] - eigenValues[0])
+ / (eigenValues[2] - haeb[0]));
return haeb;
case 7: // eulerzyz
- // TODO
- return null;
+ return Quaternion.getQuaternionFrame(P3.new3(0, 0, 0),
+ eigenVectors[0], eigenVectors[1]).getEulerZYZ();
case 8: // eulerzxz
- // TODO
- return null;
+ return Quaternion.getQuaternionFrame(P3.new3(0, 0, 0),
+ eigenVectors[0], eigenVectors[1]).getEulerZXZ();
case 9: //
- return new int[] {modelIndex, atomIndex1, atomIndex2};
+ return new int[] { modelIndex, atomIndex1, atomIndex2 };
case 10:
return type;
default:
- return null;
+ return null;
}
}
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