Revision: 18553
http://sourceforge.net/p/jmol/code/18553
Author: hansonr
Date: 2013-08-12 20:17:37 +0000 (Mon, 12 Aug 2013)
Log Message:
-----------
___JmolVersion="13.2.4_dev_2013.08.12"
bug fix: set loglevel 6 (debugHigh) not working
bug fix: {*}.tensor("", "id") not implemented
bug fix: {*}.tensor("") not implemented
bug fix: {*}.tensor("adp") fails
bug fix: {*}.symmetry fails when space group is P1
bug fix: atom tensors lost when merging
Modified Paths:
--------------
branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/MagresReader.java
branches/v13_2/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
branches/v13_2/Jmol/src/org/jmol/api/JmolNMRInterface.java
branches/v13_2/Jmol/src/org/jmol/modelset/Atom.java
branches/v13_2/Jmol/src/org/jmol/modelset/AtomCollection.java
branches/v13_2/Jmol/src/org/jmol/modelset/Measurement.java
branches/v13_2/Jmol/src/org/jmol/modelset/MeasurementData.java
branches/v13_2/Jmol/src/org/jmol/modelset/ModelCollection.java
branches/v13_2/Jmol/src/org/jmol/quantum/NMRCalculation.java
branches/v13_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java
branches/v13_2/Jmol/src/org/jmol/shape/Measures.java
branches/v13_2/Jmol/src/org/jmol/shapespecial/Ellipsoid.java
branches/v13_2/Jmol/src/org/jmol/symmetry/UnitCell.java
branches/v13_2/Jmol/src/org/jmol/util/Logger.java
branches/v13_2/Jmol/src/org/jmol/util/Tensor.java
branches/v13_2/Jmol/src/org/jmol/util/V3.java
branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties
Modified:
branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
2013-08-12 20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
2013-08-12 20:17:37 UTC (rev 18553)
@@ -572,7 +572,7 @@
for (int p = 0, i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
a[i][j] = data[p++];
- atom.addTensor(Tensor.getTensorFromAsymmetricTensor(a, "charge"), null);
+ atom.addTensor(Tensor.getTensorFromAsymmetricTensor(a, "charge",
atom.atomName + " " + line0), null);
if (!haveCharges)
appendLoadNote("Ellipsoids set \"charge\": Born Effective Charges");
haveCharges = true;
Modified:
branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2013-08-12 20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2013-08-12 20:17:37 UTC (rev 18553)
@@ -1022,7 +1022,7 @@
atoms[index].addTensor(Tensor.getTensorFromEigenVectors(directLatticeVectors,
new float[] {parseFloatStr(tokens[1]),
parseFloatStr(tokens[3]),
- parseFloatStr(tokens[5]) }, "unknown"), null);
+ parseFloatStr(tokens[5]) }, "unknown", atoms[index].atomName),
null);
readLine();
}
return true;
Modified:
branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/MagresReader.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/MagresReader.java
2013-08-12 20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/MagresReader.java
2013-08-12 20:17:37 UTC (rev 18553)
@@ -273,36 +273,39 @@
*/
private boolean readTensor() throws Exception {
String[] tokens = getTokens();
- String id = tokens[0];
- String units = magresUnits.get(id);
+ String type = tokens[0];
+ String units = magresUnits.get(type);
if (units == null) {
- Logger.warn(id + " ignored; no units defined; line: " + line);
+ Logger.warn(type + " ignored; no units defined; line: " + line);
return true;
}
- boolean isIsc = id.startsWith("isc");
+ boolean isIsc = type.startsWith("isc");
if (tokens.length == 10) {
// raw vector - you get ONE
- magresUnits.remove(id);
+ magresUnits.remove(type);
float[] data = new float[9];
for (int i = 0; i < 9;)
data[i] = parseFloatStr(tokens[++i]);
- Logger.info("Magres reader creating magres_" + id + ": " +
Escape.eAF(data));
- atomSetCollection.setAtomSetAuxiliaryInfo("magres_" + id, data);
+ Logger.info("Magres reader creating magres_" + type + ": " +
Escape.eAF(data));
+ atomSetCollection.setAtomSetAuxiliaryInfo("magres_" + type, data);
}
String atomName1 = getAtomName(tokens[1], tokens[2]);
int pt = 3;
String atomName2 = (isIsc ? getAtomName(tokens[pt++], tokens[pt++]) :
null);
if (atomName1.equals(atomName2)) {
- Logger.warn(id + " ignored; atom1 == atom2 for " + atomName1 + " line: "
+ line);
+ Logger.warn(type + " ignored; atom1 == atom2 for " + atomName1 + " line:
" + line);
return true;
}
+ String id = atomName1;
+ if (atomName2 != null)
+ id += "//" + atomName2;
double[][] a = new double[3][3];
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
a[i][j] = Double.valueOf(tokens[pt++]).doubleValue();
int index1 = atomSetCollection.getAtomIndexFromName(atomName1);
int index2;
- Tensor t = Tensor.getTensorFromAsymmetricTensor(a, id);
+ Tensor t = Tensor.getTensorFromAsymmetricTensor(a, type, id);
if (atomName2 == null) {
index2 = -1;
atomSetCollection.getAtoms()[index1].addTensor(t, null);
Modified:
branches/v13_2/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-08-12 20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-08-12 20:17:37 UTC (rev 18553)
@@ -1353,7 +1353,9 @@
float d2 = cartesian.distanceSquared(cartesians[j]);
if (checkSpecial && d2 < 0.0001) {
special = atoms[iAtomFirst + j];
- break;
+ if (special.atomName == null ||
special.atomName.equals(atoms[i].atomName))
+ break;
+ special = null;
}
if (checkRange111 && j < baseCount && d2 < minDist2)
minDist2 = d2;
@@ -1398,7 +1400,7 @@
eigenVectors = symmetry.rotateEllipsoid(iSym, ptTemp,
eigenVectors, ptTemp1, ptTemp2);
atom1.addTensor(Tensor.getTensorFromEigenVectors(eigenVectors,
- t.eigenValues, t.type), null);
+ t.eigenValues, t.isIsotropic ? "iso" : t.type, t.id), null);
}
}
}
Modified: branches/v13_2/Jmol/src/org/jmol/api/JmolNMRInterface.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/api/JmolNMRInterface.java 2013-08-12
20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/api/JmolNMRInterface.java 2013-08-12
20:17:37 UTC (rev 18553)
@@ -82,7 +82,7 @@
public JmolList<Object> getTensorInfo(String tensorType, String infoType, BS
bs);
- public Map<String, Float> getMinDistances(MeasurementData md);
+ public Map<String, Integer> getMinDistances(MeasurementData md);
public boolean getState(SB sb);
Modified: branches/v13_2/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/modelset/Atom.java 2013-08-12 20:16:55 UTC
(rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/modelset/Atom.java 2013-08-12 20:17:37 UTC
(rev 18553)
@@ -293,7 +293,9 @@
public float getADPMinMax(boolean isMax) {
Tensor[] tensors = getTensors();
- return (tensors == null || tensors[0] == null || tensors[0].iType !=
Tensor.TYPE_ADP? 0 : tensors[0].getFactoredValue(isMax ? 2 : 1));
+ Tensor t;
+ return (tensors == null || (t = tensors[0]) == null
+ || t.iType != Tensor.TYPE_ADP ? 0 : t.getFactoredValue(isMax ? 2 : 1));
}
public Tensor[] getTensors() {
@@ -725,7 +727,7 @@
for (int j = 0; j < nOps; j++)
if (atomSymmetry.get(pt++))
str += "," + (j + 1) + "" + cellRange[i];
- return str.substring(1);
+ return (str.length() == 0 ? "" : str.substring(1));
}
public int getModelIndex() {
Modified: branches/v13_2/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/modelset/AtomCollection.java
2013-08-12 20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/modelset/AtomCollection.java
2013-08-12 20:17:37 UTC (rev 18553)
@@ -104,6 +104,7 @@
ionicRadii = mergeModelSet.ionicRadii;
partialCharges = mergeModelSet.partialCharges;
atomTensors = mergeModelSet.atomTensors;
+ atomTensorList = mergeModelSet.atomTensorList;
setHaveStraightness(false);
surfaceDistance100s = null;
}
Modified: branches/v13_2/Jmol/src/org/jmol/modelset/Measurement.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/modelset/Measurement.java 2013-08-12
20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/modelset/Measurement.java 2013-08-12
20:17:37 UTC (rev 18553)
@@ -534,15 +534,15 @@
return true;
}
- public boolean isMin(Map<String, Float> htMin) {
+ public boolean isMin(Map<String, Integer> htMin) {
Atom a1 = (Atom) getAtom(1);
Atom a2 = (Atom) getAtom(2);
- float d = a2.distanceSquared(a1);
+ int d = (int) (a2.distanceSquared(a1)*100);
String n1 = a1.getAtomName();
String n2 = a2.getAtomName();
String key = (n1.compareTo(n2) < 0 ? n1 + n2 : n2 + n1);
- Float min = htMin.get(key);
- return (min != null && d == min.floatValue());
+ Integer min = htMin.get(key);
+ return (min != null && d == min.intValue());
}
}
Modified: branches/v13_2/Jmol/src/org/jmol/modelset/MeasurementData.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/modelset/MeasurementData.java
2013-08-12 20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/modelset/MeasurementData.java
2013-08-12 20:17:37 UTC (rev 18553)
@@ -83,7 +83,7 @@
/*
* the general constructor. tokAction is not used here
*/
- public MeasurementData set(int tokAction, Map<String, Float> htMin,
+ public MeasurementData set(int tokAction, Map<String, Integer> htMin,
RadiusData radiusData, String strFormat, String
units,
TickInfo tickInfo,
boolean mustBeConnected, boolean mustNotBeConnected,
@@ -161,7 +161,7 @@
private Viewer viewer;
private int iFirstAtom;
private boolean justOneModel = true;
- public Map<String, Float> htMin;
+ public Map<String, Integer> htMin;
/**
* called by the client to generate a set of measurements
Modified: branches/v13_2/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/modelset/ModelCollection.java
2013-08-12 20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/modelset/ModelCollection.java
2013-08-12 20:17:37 UTC (rev 18553)
@@ -3102,7 +3102,7 @@
if (partialCharges != null)
for (int i = i0; i < atomCount; i++)
partialCharges[i] = partialCharges[map[i]];
- if (atomTensors != null) {
+ if (atomTensorList != null) {
for (int i = i0; i < atomCount; i++) {
Tensor[] list = atomTensorList[i] = atomTensorList[map[i]];
for (int j = list.length; --j >= 0;) {
@@ -3134,7 +3134,7 @@
bfactor100s = ArrayUtil.arrayCopyShort(bfactor100s, newLength);
if (partialCharges != null)
partialCharges = ArrayUtil.arrayCopyF(partialCharges, newLength);
- if (atomTensors != null)
+ if (atomTensorList != null)
atomTensorList = (Tensor[][]) ArrayUtil.arrayCopyObject(atomTensorList,
newLength);
if (atomNames != null)
atomNames = ArrayUtil.arrayCopyS(atomNames, newLength);
Modified: branches/v13_2/Jmol/src/org/jmol/quantum/NMRCalculation.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/quantum/NMRCalculation.java
2013-08-12 20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/quantum/NMRCalculation.java
2013-08-12 20:17:37 UTC (rev 18553)
@@ -35,6 +35,7 @@
import org.jmol.io.JmolBinary;
import org.jmol.modelset.Atom;
import org.jmol.modelset.MeasurementData;
+import org.jmol.modelset.Model;
import org.jmol.util.BS;
import org.jmol.util.Escape;
import org.jmol.util.JmolList;
@@ -87,40 +88,64 @@
}
/**
- * Returns a list of tensors that are of the specified type and
- * have both atomIndex1 and atomIndex2 in bs.
+ * Returns a list of tensors that are of the specified type and have both
+ * atomIndex1 and atomIndex2 in bsA. If there is just one atom specified,
then
+ * the list is "all tensors involving this atom".
*
+ * We have to use atom sites, because interaction tensors are not duplicated.
+ *
* @param type
- * @param bs
- * @param bs2
+ * @param bsA
* @return list of Tensors
*/
@SuppressWarnings("unchecked")
- private JmolList<Tensor> getInteractionTensorList(String type, BS bs, BS
bs2) {
- type = type.toLowerCase();
- BS bsModels = viewer.getModelBitSet(bs, false);
- int iAtom = (bs.cardinality() == 1 ? bs.nextSetBit(0) : -1);
+ private JmolList<Tensor> getInteractionTensorList(String type, BS bsA) {
+ if (type != null)
+ type = type.toLowerCase();
+ BS bsModels = viewer.getModelBitSet(bsA, false);
+ BS bs1 = getAtomSiteBS(bsA);
+ int iAtom = (bs1.cardinality() == 1 ? bs1.nextSetBit(0) : -1);
JmolList<Tensor> list = new JmolList<Tensor>();
for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i +
1)) {
- JmolList<Tensor> tensors = (JmolList<Tensor>)
viewer.getModelAuxiliaryInfoValue(i, "interactionTensors");
+ JmolList<Tensor> tensors = (JmolList<Tensor>) viewer
+ .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)
- && t.isSelected(bs, iAtom)
- && (bs2 == null || bs2.get(getOtherAtom(t, iAtom))))
-
+ if (type == null || t.type.equals(type) && t.isSelected(bs1, iAtom))
list.addLast(t);
- }
+ }
}
return list;
}
- private int getOtherAtom(Tensor t, int iAtom) {
- return (t.atomIndex1 == iAtom ? t.atomIndex2 : t.atomIndex1);
+ /**
+ * Interaction tensors are not repeated for every possible combination. They
are just for the
+ * base atom set. These are identified as a.atomIndex ==
models[b.modelIndex].firstAtomIndex + b.atomSite - 1
+ * @param bsA
+ * @return new bs in terms of atom sites
+ */
+ private BS getAtomSiteBS(BS bsA) {
+ if (bsA == null)
+ return null;
+ BS bs = new BS();
+ Atom[] atoms = viewer.modelSet.atoms;
+ Model[] models = viewer.modelSet.models;
+
+ for (int i = bsA.nextSetBit(0); i >= 0; i = bsA.nextSetBit(i + 1)) {
+ if (!bsA.get(i))
+ continue;
+ Atom a = atoms[i];
+ bs.set(models[a.modelIndex].firstAtomIndex - 1 + a.atomSite);
+ }
+ return bs;
}
+
+// private int getOtherAtom(Tensor t, int iAtom) {
+// return (t.atomIndex1 == iAtom ? t.atomIndex2 : t.atomIndex1);
+// }
public BS getUniqueTensorSet(BS bsAtoms) {
BS bs = new BS();
@@ -176,11 +201,9 @@
if (type == null || a1.modelIndex != a2.modelIndex)
return 0;
BS bs = new BS();
- BS bs2 = new BS();
- int i0 = viewer.modelSet.models[a1.modelIndex].firstAtomIndex - 1;
- bs.set(a1.atomSite + i0);
- bs2.set(a2.atomSite + i0);
- JmolList<Tensor> list = getInteractionTensorList(type, bs, bs2);
+ bs.set(a1.index);
+ bs.set(a2.index);
+ JmolList<Tensor> list = getInteractionTensorList(type, bs);
if (list.size() == 0)
return Float.NaN;
isc = list.get(0);
@@ -216,8 +239,7 @@
}
public float getDipolarCouplingHz(Atom a1, Atom a2, V3 vField) {
- V3 v12 = V3.newV(a2);
- v12.sub(a1);
+ V3 v12 = V3.newVsub(a2, a1);
double r = v12.length();
double costheta = v12.dot(vField) / r / vField.length();
return (float) (getDipolarConstantHz(a1, a2) * (3 * costheta - 1) / 2);
@@ -369,10 +391,11 @@
public JmolList<Object> getTensorInfo(String tensorType, String infoType,
BS bs) {
-
+ if ("".equals(tensorType))
+ tensorType = null;
JmolList<Object> data = new JmolList<Object>();
JmolList<Object> list1;
- if (infoType.equals(";dc.")) {
+ if (";dc.".equals(infoType)) {
// tensorType is irrelevant for dipolar coupling constant
Atom[] atoms = viewer.modelSet.atoms;
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
@@ -384,9 +407,11 @@
.addLast(Float.valueOf(getDipolarConstantHz(atoms[i],
atoms[j])));
data.addLast(list1);
}
- } else if (tensorType.startsWith("isc")) {
+ return data;
+ }
+ if (tensorType == null || tensorType.startsWith("isc")) {
boolean isJ = infoType.equals(";j.");
- JmolList<Tensor> list = getInteractionTensorList(tensorType, bs, null);
+ JmolList<Tensor> list = getInteractionTensorList(tensorType, bs);
int n = (list == null ? 0 : list.size());
for (int i = 0; i < n; i++) {
Tensor t = list.get(i);
@@ -397,9 +422,17 @@
: t.getInfo(infoType));
data.addLast(list1);
}
- } else {
- boolean isChi = tensorType.startsWith("efg") && infoType.equals(";chi.");
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ if (tensorType != null)
+ return data;
+ }
+ boolean isChi = tensorType != null && tensorType.startsWith("efg")
+ && infoType.equals(";chi.");
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ if (tensorType == null) {
+ Tensor[] a = viewer.modelSet.getAtomTensorList(i);
+ for (int j = 0; j < a.length; j++)
+ data.addLast(a[j].getInfo(infoType));
+ } else {
Tensor t = viewer.modelSet.getAtomTensor(i, tensorType);
data.addLast(t == null ? null : isChi ? Float
.valueOf(getQuadrupolarConstant(t)) : t.getInfo(infoType));
@@ -408,7 +441,7 @@
return data;
}
- public Map<String, Float> getMinDistances(MeasurementData md) {
+ public Map<String, Integer> getMinDistances(MeasurementData md) {
BS bsPoints1 = (BS) md.points.get(0);
int n1 = bsPoints1.cardinality();
if (n1 == 0 || !(md.points.get(1) instanceof BS))
@@ -417,7 +450,7 @@
int n2 = bsPoints2.cardinality();
if (n1 < 2 && n2 < 2)
return null;
- Map<String, Float> htMin = new Hashtable<String, Float>();
+ Map<String, Integer> htMin = new Hashtable<String, Integer>();
Atom[] atoms = viewer.modelSet.atoms;
for (int i = bsPoints1.nextSetBit(0); i >= 0; i = bsPoints1
.nextSetBit(i + 1)) {
@@ -426,19 +459,19 @@
for (int j = bsPoints2.nextSetBit(0); j >= 0; j = bsPoints2
.nextSetBit(j + 1)) {
Atom a2 = atoms[j];
- float d = a2.distanceSquared(a1);
+ int d = (int) (a2.distanceSquared(a1) * 100);
if (d == 0)
continue;
String name1 = a2.getAtomName();
String key = (name.compareTo(name1) < 0 ? name + name1 : name1 + name);
- Float min = htMin.get(key);
+ Integer min = htMin.get(key);
if (min == null) {
- min = Float.valueOf(d);
+ min = Integer.valueOf(d);
htMin.put(key, min);
continue;
}
- if (d < min.floatValue())
- htMin.put(key, Float.valueOf(d));
+ if (d < min.intValue())
+ htMin.put(key, Integer.valueOf(d));
}
}
return htMin;
Modified: branches/v13_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2013-08-12 20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2013-08-12 20:17:37 UTC (rev 18553)
@@ -835,17 +835,18 @@
}
private boolean evaluateTensor(SV[] args) throws ScriptException {
+ // {*}.tensor()
+ // {*}.tensor("isc") // only within this atom set
+ // {atomindex=1}.tensor("isc") // all to this atom
// {*}.tensor("efg","eigenvalues")
- // T.tensor is set to allow exactly 2 parameters
- // change that in T.java to adjust
- if (args.length == 0 || args.length > 2)
+ if (args.length > 2)
return false;
BS bs = SV.getBitSet(getX(), false);
- String tensorType = SV.sValue(args[0]).toLowerCase();
+ String tensorType = (args.length == 0 ? null :
SV.sValue(args[0]).toLowerCase());
String infoType = ";"
- + (args.length == 1 ? "all" : SV.sValue(args[1]).toLowerCase()) + ".";
+ + (args.length < 2 ? "all" : SV.sValue(args[1]).toLowerCase()) + ".";
JmolNMRInterface calc = viewer.getNMRCalculation();
- if (tensorType.equals("unique"))
+ if ("unique".equals(tensorType))
return addXBs(calc.getUniqueTensorSet(bs));
return addXList(calc.getTensorInfo(tensorType, infoType, bs));
}
Modified: branches/v13_2/Jmol/src/org/jmol/shape/Measures.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/shape/Measures.java 2013-08-12
20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/shape/Measures.java 2013-08-12
20:17:37 UTC (rev 18553)
@@ -67,7 +67,7 @@
TickInfo tickInfo;
TickInfo defaultTickInfo;
public JmolFont font3d;
- private Map<String, Float> htMin;
+ private Map<String, Integer> htMin;
@Override
protected void initModelSet() {
Modified: branches/v13_2/Jmol/src/org/jmol/shapespecial/Ellipsoid.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/shapespecial/Ellipsoid.java
2013-08-12 20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/shapespecial/Ellipsoid.java
2013-08-12 20:17:37 UTC (rev 18553)
@@ -128,7 +128,7 @@
protected void setEquation(double[] coef) {
isValid = false;
- tensor = Tensor.getTensorFromThermalEquation(coef);
+ tensor = Tensor.getTensorFromThermalEquation(coef, null);
validate(true);
}
Modified: branches/v13_2/Jmol/src/org/jmol/symmetry/UnitCell.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/symmetry/UnitCell.java 2013-08-12
20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/symmetry/UnitCell.java 2013-08-12
20:17:37 UTC (rev 18553)
@@ -26,6 +26,7 @@
package org.jmol.symmetry;
import org.jmol.util.BoxInfo;
+import org.jmol.util.Escape;
import org.jmol.util.Matrix3f;
import org.jmol.util.Matrix4f;
import org.jmol.util.P3;
@@ -307,7 +308,7 @@
float[] eigenValues = new float[] {f, f, f};
// sqrt will be taken when converted to lengths later
// no factor of 0.5 pi^2
- return Tensor.getTensorFromEigenVectors(unitVectors, eigenValues, "iso");
+ return Tensor.getTensorFromEigenVectors(unitVectors, eigenValues, "iso",
"Uiso=" + f);
}
double[] Bcart = new double[6];
@@ -367,7 +368,7 @@
//System.out.println("UnitCell Bcart=" + Bcart[0] + " " + Bcart[1] + " "
// + Bcart[2] + " " + Bcart[3] + " " + Bcart[4] + " " + Bcart[5]);
- return Tensor.getTensorFromThermalEquation(Bcart);
+ return Tensor.getTensorFromThermalEquation(Bcart, Escape.eAF(parBorU));
}
P3[] getCanonicalCopy(float scale) {
Modified: branches/v13_2/Jmol/src/org/jmol/util/Logger.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/util/Logger.java 2013-08-12 20:16:55 UTC
(rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/util/Logger.java 2013-08-12 20:17:37 UTC
(rev 18553)
@@ -110,6 +110,7 @@
level = LEVEL_MAX - 1;
_activeLevels[level] = active;
debugging = isActiveLevel(LEVEL_DEBUG) || isActiveLevel(LEVEL_DEBUGHIGH);
+ debuggingHigh = (debugging && _activeLevels[LEVEL_DEBUGHIGH]);
}
/**
Modified: branches/v13_2/Jmol/src/org/jmol/util/Tensor.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/util/Tensor.java 2013-08-12 20:16:55 UTC
(rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/util/Tensor.java 2013-08-12 20:17:37 UTC
(rev 18553)
@@ -45,8 +45,10 @@
private static EigenSort tSort; // used for sorting eigenvector/values
+
// base data:
+ public String id;
public String type;
public int iType = TYPE_OTHER;
@@ -120,7 +122,8 @@
+ ";asymmatrix..." + ";symmatrix...." + ";value........"
+ ";isotropy....." + ";anisotropy..." + ";asymmetry...."
+ ";eulerzyz....." + ";eulerzxz....." + ";quaternion..."
- + ";indices......" + ";string......." + ";type.........";
+ + ";indices......" + ";string......." + ";type........."
+ + ";id...........";
/**
* returns an object of the specified type, including "eigenvalues",
* "eigenvectors", "asymmetric", "symmetric", "trace", "indices", and "type"
@@ -137,8 +140,11 @@
Map<String, Object> info = new Hashtable<String, Object>();
String[] s = Parser.getTokens(TextFormat.replaceAllCharacter(infoList,
";.", ' ').trim());
Arrays.sort(s);
- for (int i = 0; i < s.length; i++)
- info.put(s[i], getInfo(s[i]));
+ for (int i = 0; i < s.length; i++) {
+ Object o = getInfo(s[i]);
+ if (o != null)
+ info.put(s[i], o);
+ }
return info;
case 1:
@@ -195,6 +201,9 @@
return this.toString();
case 14:
return type;
+
+ case 15:
+ return id;
}
}
@@ -222,6 +231,7 @@
t.modelIndex = t0.modelIndex;
t.atomIndex1 = t0.atomIndex1;
t.atomIndex2 = t0.atomIndex2;
+ t.id = t0.id;
return t;
}
@@ -237,9 +247,10 @@
*
* @param asymmetricTensor
* @param type
+ * @param id
* @return Tensor
*/
- public static Tensor getTensorFromAsymmetricTensor(double[][]
asymmetricTensor, String type) {
+ public static Tensor getTensorFromAsymmetricTensor(double[][]
asymmetricTensor, String type, String id) {
double[][] a = new double[3][3];
for (int i = 3; --i >= 0;)
for (int j = 3; --j >= 0;)
@@ -284,9 +295,10 @@
V3[] vectors = new V3[3];
float[] values = new float[3];
eigen.fillArrays(vectors, values);
- Tensor t = newTensorType(vectors, values, type);
+ Tensor t = newTensorType(vectors, values, type, id);
t.asymMatrix = asymmetricTensor;
t.symMatrix = a;
+ t.id = id;
return t;
}
@@ -296,17 +308,18 @@
* @param eigenVectors
* @param eigenValues
* @param type
+ * @param id
* @return Tensor
*/
public static Tensor getTensorFromEigenVectors(V3[] eigenVectors,
- float[] eigenValues, String type) {
+ float[] eigenValues, String type,
String id) {
float[] values = new float[3];
V3[] vectors = new V3[3];
for (int i = 0; i < 3; i++) {
vectors[i] = V3.newV(eigenVectors[i]);
values[i] = eigenValues[i];
}
- return newTensorType(vectors, values, type);
+ return newTensorType(vectors, values, type, id);
}
/**
@@ -340,12 +353,14 @@
* (see http://www.iucr.org/iucr-top/comm/cnom/adp/finrepone/finrepone.html)
*
* @param coefs
+ * @param id
* @return Tensor
*/
- public static Tensor getTensorFromThermalEquation(double[] coefs) {
+ public static Tensor getTensorFromThermalEquation(double[] coefs, String id)
{
Tensor t = new Tensor();
t.eigenValues = new float[3];
t.eigenVectors = new V3[3];
+ t.id = (id == null ? "coefs=" + Escape.eAD(coefs) : id);
// assumes an ellipsoid centered on 0,0,0
// called by UnitCell for the initial creation from PDB/CIF ADP data
double[][] mat = new double[3][3];
@@ -406,15 +421,17 @@
* @param vectors
* @param values
* @param type
+ * @param id
* @return Tensor
*/
- private static Tensor newTensorType(V3[] vectors, float[] values, String
type) {
+ private static Tensor newTensorType(V3[] vectors, float[] values, String
type, String id) {
Tensor t = new Tensor();
t.eigenValues = values;
t.eigenVectors = vectors;
for (int i = 0; i < 3; i++)
t.eigenVectors[i].normalize();
t.setType(type);
+ t.id = id;
t.sortAndNormalize();
t.eigenSignMask = (t.eigenValues[0] >= 0 ? 1 : 0)
+ (t.eigenValues[1] >= 0 ? 2 : 0) + (t.eigenValues[2] >= 0 ? 4 : 0);
Modified: branches/v13_2/Jmol/src/org/jmol/util/V3.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/util/V3.java 2013-08-12 20:16:55 UTC
(rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/util/V3.java 2013-08-12 20:17:37 UTC
(rev 18553)
@@ -33,13 +33,13 @@
public class V3 extends Tuple3f {
public static V3 newV(Tuple3f t) {
- V3 v = new V3();
- v.x = t.x;
- v.y = t.y;
- v.z = t.z;
- return v;
+ return V3.new3(t.x, t.y, t.z);
}
+ public static V3 newVsub(Tuple3f t1, Tuple3f t2) {
+ return V3.new3(t1.x - t2.x, t1.y - t2.y,t1.z - t2.z);
+ }
+
public static V3 new3(float x, float y, float z) {
V3 v = new V3();
v.x = x;
Modified: branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-12
20:16:55 UTC (rev 18552)
+++ branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-12
20:17:37 UTC (rev 18553)
@@ -9,8 +9,15 @@
# Don't use ___ in your text, as that is the key for stripping out
# the information saved in the JAR version of this file.
-___JmolVersion="13.2.4_dev_2013.08.10"
+___JmolVersion="13.2.4_dev_2013.08.12"
+bug fix: set loglevel 6 (debugHigh) not working
+bug fix: {*}.tensor("", "id") not implemented
+bug fix: {*}.tensor("") not implemented
+bug fix: {*}.tensor("adp") fails
+bug fix: {*}.symmetry fails when space group is P1
+bug fix: atom tensors lost when merging
+
bug fix: float parser broken in dev_2013.08.07
bug fix: zoom setting lost in state
bug fix: shapeInfo not reporting visibility of isosurface
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