Revision: 18383
http://sourceforge.net/p/jmol/code/18383
Author: hansonr
Date: 2013-07-01 08:08:21 +0000 (Mon, 01 Jul 2013)
Log Message:
-----------
___JmolVersion="13.1.19_dev_2013.07.01"
new feature: {xxx}.tensor(type,what)
-- type = "temp", "ms", "efg", etc.
-- what = "eigenvalues", "eigenvectors", "asymmetric", "symmetric", "type",
and "indices"
-- returns a list of data
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.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
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-06-30
07:21:27 UTC (rev 18382)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-07-01
08:08:21 UTC (rev 18383)
@@ -250,6 +250,17 @@
return (i < 0 || atomTensorList == null || i >= atomTensorList.length ?
null
: atomTensorList[i]);
}
+
+ public Tensor getAtomTensor(int i, String type) {
+ Tensor[] tensors = getAtomTensorList(i);
+ if (tensors == null || type == null)
+ return null;
+ type = type.toLowerCase();
+ for (int j = 0; j < tensors.length; j++)
+ if (tensors[j] != null && type.equals(tensors[j].type))
+ return tensors[j];
+ return null;
+ }
protected void setAtomTensors(int atomIndex, JmolList<Tensor> list) {
if (list == null || list.size() == 0)
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-06-30
07:21:27 UTC (rev 18382)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-07-01
08:08:21 UTC (rev 18383)
@@ -3419,5 +3419,24 @@
return ilist;
}
+ @SuppressWarnings("unchecked")
+ public JmolList<Tensor> getInteractionTensorList(String type, BS bs) {
+ type = type.toLowerCase();
+ BS bsModels = getModelBitSet(bs, false);
+ JmolList<Tensor> list = new JmolList<Tensor>();
+ for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i +
1)) {
+ JmolList<Tensor> tensors = (JmolList<Tensor>)
getModelAuxiliaryInfoValue(i, "interactionTensors");
+ if (tensors == null)
+ continue;
+ int n = tensors.size();
+ for (int j = 0; j < n; j++) {
+ Tensor t = tensors.get(j);
+ if (t.type.equals(type))
+ list.addLast(t);
+ }
+ }
+ return list;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2013-06-30 07:21:27 UTC
(rev 18382)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2013-07-01 08:08:21 UTC
(rev 18383)
@@ -37,7 +37,6 @@
import org.jmol.util.P4;
import org.jmol.util.Quaternion;
import org.jmol.util.SB;
-import org.jmol.util.Tensor;
import org.jmol.util.Tuple3f;
import org.jmol.util.V3;
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-06-30
07:21:27 UTC (rev 18382)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-01
08:08:21 UTC (rev 18383)
@@ -61,6 +61,7 @@
import org.jmol.util.P4;
import org.jmol.util.Quaternion;
import org.jmol.util.SB;
+import org.jmol.util.Tensor;
import org.jmol.util.TextFormat;
import org.jmol.util.Tuple3f;
import org.jmol.util.V3;
@@ -821,6 +822,8 @@
return evaluateSymop(args, op.tok == T.propselector);
// case Token.volume:
// return evaluateVolume(args);
+ case T.tensor:
+ return evaluateTensor(args);
case T.within:
return evaluateWithin(args);
case T.contact:
@@ -831,6 +834,28 @@
return false;
}
+ private boolean evaluateTensor(SV[] args) throws ScriptException {
+ // {*}.tensor("efg","eigenvalues")
+ // T.tensor is set to allow exactly 2 parameters
+ // change that in T.java to adjust
+ BS bs = SV.getBitSet(getX(), false);
+ String tensorType = SV.sValue(args[0]).toLowerCase();
+ String infoType = ";" + SV.sValue(args[1]).toLowerCase() + ".";
+ JmolList<Object> data = new JmolList<Object>();
+ if (tensorType.equals("isc")) {
+ JmolList<Tensor> list = viewer.modelSet.getInteractionTensorList("isc",
+ bs);
+ int n = (list == null ? 0 : list.size());
+ for (int i = 0; i < n; i++)
+ data.addLast((list.get(i).getInfo(infoType)));
+ }
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ Tensor t = viewer.modelSet.getAtomTensor(i, tensorType);
+ data.addLast(t == null ? null : t.getInfo(infoType));
+ }
+ return addXList(data);
+ }
+
private boolean evaluateCache(SV[] args) {
if (args.length > 0)
return false;
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2013-06-30 07:21:27 UTC (rev
18382)
+++ trunk/Jmol/src/org/jmol/script/T.java 2013-07-01 08:08:21 UTC (rev
18383)
@@ -745,8 +745,8 @@
public final static int add = 1 | 2 << 9 | mathfunc | mathproperty;
public final static int distance = 2 | 2 << 9 | mathfunc | mathproperty;
- final static int find = 4 | 3 << 9 | mathfunc | mathproperty;
final static int replace = 3 | 2 << 9 | mathfunc | mathproperty;
+ final static int tensor = 4 | 2 << 9 | mathfunc | mathproperty;
// xxx(a,b,c)
@@ -759,6 +759,7 @@
final static int bin = 1 | 3 << 9 | mathfunc | mathproperty;
public final static int symop = 2 | 3 << 9 | mathfunc | mathproperty |
intproperty;
+ final static int find = 3 | 3 << 9 | mathfunc | mathproperty;
// anything beyond 3 are set "unlimited"
@@ -1978,6 +1979,7 @@
"sxyz", T.t(screenxyz),
"temperature", T.t(temperature),
"relativeTemperature", null,
+ "tensor", T.t(tensor),
"theta", T.t(theta),
"thisModel", T.t(thismodel),
"ticks", T.t(ticks),
Modified: trunk/Jmol/src/org/jmol/util/Tensor.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Tensor.java 2013-06-30 07:21:27 UTC (rev
18382)
+++ trunk/Jmol/src/org/jmol/util/Tensor.java 2013-07-01 08:08:21 UTC (rev
18383)
@@ -108,6 +108,56 @@
public int atomIndex1 = -1;
public int atomIndex2 = -1;
+ /**
+ * returns an object of the specified type, including
+ * "eigenvalues", "eigenvectors", "asymmetric", "symmetric", "type", and
"indices"
+ *
+ * @param infoType
+ * @return Object or null
+ */
+ public Object getInfo(String infoType) {
+ if (infoType.charAt(0) != ';')
+ infoType = ";" + infoType + ".";
+ switch ((";............."
+ + ";eigenvalues.."
+ + ";eigenvectors."
+ + ";asymmetric..."
+ + ";symmetric...."
+ + ";type........."
+ + ";indices......").indexOf(infoType)) {
+ case 14:
+ return eigenValues;
+ case 28:
+ P3[] list = new P3[3];
+ for (int i = 0; i < 3; i++)
+ list[i] = P3.newP(eigenVectors[i]);
+ return list;
+ case 42:
+ if (asymTensor == null)
+ return null;
+ float[][] a = new float[3][3];
+ for (int i = 0; i < 3; i++)
+ for (int j = 0; j < 3; j++)
+ a[i][j] = (float) asymTensor[i][j];
+ return a;
+ case 56:
+ if (symTensor == null)
+ return null;
+ float[][] b = new float[3][3];
+ for (int i = 0; i < 3; i++)
+ for (int j = 0; j < 3; j++)
+ b[i][j] = (float) symTensor[i][j];
+ return b;
+ case 70:
+ return type;
+ case 84:
+ return new int[] {modelIndex, atomIndex1, atomIndex2};
+ default:
+ return null;
+ }
+ }
+
+
public static Tensor copyTensor(Tensor t0) {
Tensor t = new Tensor();
t.setType(t0.type);
@@ -227,7 +277,7 @@
|| Math.abs(t.eigenVectors[1].dot(t.eigenVectors[2])) > 0.0001f
|| Math.abs(t.eigenVectors[2].dot(t.eigenVectors[0])) > 0.0001f)
return null;
- sort(t.eigenVectors, t.eigenValues);
+ sortAndNormalize(t.eigenVectors, t.eigenValues);
return t.setType("other");
}
@@ -252,7 +302,7 @@
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);
- sort(t.eigenVectors, t.eigenValues);
+ sortAndNormalize(t.eigenVectors, t.eigenValues);
t.typeFactor = TEMPERATURE_FACTOR;
return t.setType("temp");
}
@@ -304,7 +354,7 @@
t.eigenVectors = vectors;
for (int i = 0; i < 3; i++)
t.eigenVectors[i].normalize();
- sort(t.eigenVectors, t.eigenValues);
+ sortAndNormalize(t.eigenVectors, t.eigenValues);
t.setType(type);
t.eigenSignMask = (t.eigenValues[0] >= 0 ? 1 : 0)
+ (t.eigenValues[1] >= 0 ? 2 : 0) + (t.eigenValues[2] >= 0 ? 4 : 0);
@@ -363,12 +413,11 @@
*
* |sigma_3 - sigma_iso| >= |sigma_1 - sigma_iso| >= |sigma_2 - sigma_iso|
*
- * and normalize the eigenVectors
*
* @param eigenVectors
* @param eigenValues
*/
- private static void sort(V3[] eigenVectors, float[] eigenValues) {
+ private static void sortAndNormalize(V3[] eigenVectors, float[] eigenValues)
{
// 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]) },
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-30 07:21:27 UTC
(rev 18382)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-01 08:08:21 UTC
(rev 18383)
@@ -9,8 +9,13 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.19_dev_2013.06.29"
+___JmolVersion="13.1.19_dev_2013.07.01"
+new feature: {xxx}.tensor(type,what)
+ -- type = "temp", "ms", "efg", etc.
+ -- what = "eigenvalues", "eigenvectors", "asymmetric", "symmetric", "type",
and "indices"
+ -- returns a list of data
+
new feature: SET ECHO POINT {atom or point}
-- allows 2D and 3D echos to have
-- needs a bit of adjustment, as it only works when x is not within range of
echo itself (same with labels)
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