Revision: 18613
http://sourceforge.net/p/jmol/code/18613
Author: hansonr
Date: 2013-08-22 05:06:08 +0000 (Thu, 22 Aug 2013)
Log Message:
-----------
simpler expressions -- do check!
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/util/Tensor.java
Modified: trunk/Jmol/src/org/jmol/util/Tensor.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Tensor.java 2013-08-21 22:41:14 UTC (rev
18612)
+++ trunk/Jmol/src/org/jmol/util/Tensor.java 2013-08-22 05:06:08 UTC (rev
18613)
@@ -180,13 +180,13 @@
case 5: // value
return Float.valueOf(eigenValues[2]);
case 6: // isotropy
- return Float.valueOf(getIso());
+ return Float.valueOf(iso());
case 7: // anisotropy
// Anisotropy, defined as Vzz-(Vxx+Vyy)/2
- return Float.valueOf(getAnisotropy());
+ return Float.valueOf(anisotropy());
case 8: // asymmetry
// Asymmetry, defined as (Vyy-Vxx)/(Vzz - Viso)
- return Float.valueOf(getAsymmetry());
+ return Float.valueOf(asymmetry());
case 9: // eulerzyz
@@ -209,43 +209,125 @@
return id;
case 16:
- return Float.valueOf(getSpan());
+ return Float.valueOf(span());
case 17:
- return Float.valueOf(getSkew());
+ return Float.valueOf(skew());
}
}
- public float getIso() {
+ // | | |
+ // | | |
+ // e2 e1 e0
+ // |
+ // iso
+
+ /**
+ * isotropy = average of eigenvalues
+ *
+ * @return isotropy
+ */
+ public float iso() {
return (eigenValues[0] + eigenValues[1] + eigenValues[2]) / 3;
}
- public float getAnisotropy() {
- return eigenValues[2] - (eigenValues[0] + eigenValues[1]) / 2;
+ // | | |
+ // | | |
+ // e2 e1 e0
+ // |---------------------------|
+ // span
+ //
+ // span = |e2 - e0|
+ //
+
+ /**
+ * width of the signal; |e2 - e0|
+ *
+ * @return unitless; >= 0
+ */
+ public float span() {
+ return Math.abs(eigenValues[2] - eigenValues[0]);
}
- public float getAsymmetry() {
- return eigenValues[0] == eigenValues[2] ? 0 : (eigenValues[1] -
eigenValues[0])
- / (eigenValues[2] - getIso());
- }
+
- public float getSpan() {
- float red_aniso = eigenValues[2]-getIso();
- float asymm = getAsymmetry();
+ // | | |
+ // | | |
+ // e2 | e1 e0
+ // iso
+ //
+ // |---------------------------|
+ // span
+ //
+ // skew = 3 (e1 - iso) / span
+ //
+ // or 0 if 0/0
- if (red_aniso > 0.0)
- return red_aniso*(3.0f+asymm)/2.0f;
+ /**
+ * a measure of asymmetry.
+ *
+ * @return range [-1, 1]
+ */
+ public float skew() {
+ return (span() == 0 ? 0 : 3 * (eigenValues[1] - iso()) / span());
+ }
- return -red_aniso*(3.0f+asymm)/2.0f;
+
+ // anistropy = e2 - (e1 + e0)/2
+ //
+ // | | |
+ // | | |
+ // e2 e1 e0
+ // <----------------------|
+ // anisotropy
+
+ /**
+ * anisotropy = directed distance from (center of two closest) to (the
furthest)
+ * @return unitless number
+ */
+ public float anisotropy() {
+ return eigenValues[2] - (eigenValues[0] + eigenValues[1]) / 2;
}
-
- public float getSkew() {
- float red_aniso = eigenValues[2]-getIso();
- float asymm = getAsymmetry();
- return -3.0f*red_aniso*(1.0f-asymm)/2.0f/getSpan();
+ // reduced anisotropy = e2 - iso = anisotropy * 2/3
+ //
+ // | | |
+ // | | |
+ // e2 iso e1 e0
+ // <----------------------|
+ // anisotropy
+ // <--------------|
+ // reduced anisotropy
+
+ /**
+ * reduced anisotropy = largest difference from isotropy
+ * (may be negative)
+ *
+ * @return unitless number
+ *
+ */
+ public float redAniso() {
+ return anisotropy() * 2 / 3; // = eigenValues[2]-iso();
}
+ // asymmetry = d10/ra
+ //
+ // | | |
+ // | | |
+ // e2 iso e1 e0
+ // <--------------| <--------|
+ // ra d10
+ // or 0 when 0/0
+
+ /**
+ * asymmetry = deviation from a symmetric tensor
+ *
+ * @return range [0,1]
+ */
+ public float asymmetry() {
+ return span() == 0 ? 0 : (eigenValues[1] - eigenValues[0]) / redAniso();
+ }
+
public static Tensor copyTensor(Tensor t0) {
Tensor t = new Tensor();
t.setType(t0.type);
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