Revision: 18552
http://sourceforge.net/p/jmol/code/18552
Author: hansonr
Date: 2013-08-12 20:16:55 +0000 (Mon, 12 Aug 2013)
Log Message:
-----------
___JmolVersion="13.3.4_dev_2013.08.12"
new feature: incommensurate modulation of ADPs.
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:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagresReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java
trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
trunk/Jmol/src/org/jmol/script/SV.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/shapespecial/Ellipsoid.java
trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/symmetry/UnitCell.java
trunk/Jmol/src/org/jmol/util/Logger.java
trunk/Jmol/src/org/jmol/util/Modulation.java
trunk/Jmol/src/org/jmol/util/ModulationSet.java
trunk/Jmol/src/org/jmol/util/Tensor.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/openscience/jmol/app/surfacetool/SurfaceTool.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-12
02:02:51 UTC (rev 18551)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-12
20:16:55 UTC (rev 18552)
@@ -42,7 +42,6 @@
import org.jmol.util.BS;
-import org.jmol.util.Escape;
import org.jmol.util.Logger;
import org.jmol.util.Matrix4f;
import org.jmol.util.P3;
@@ -239,7 +238,6 @@
String key = TextFormat.simpleReplace(auditBlockCode, "_MOD_",
"_REFRNCE_");
if ((atomSetCollection.symmetry = (SymmetryInterface)
htAudit.get(key)) != null) {
notionalUnitCell =
atomSetCollection.symmetry.getNotionalUnitCell();
- System.out.println(Escape.eAF(notionalUnitCell));
iHaveUnitCell = true;
}
} else if (htAudit != null && symops != null) {
@@ -2510,6 +2508,8 @@
continue;
if (id.equals("D_S")) {
// saw tooth displacement center/width/Axyz
+ if (Float.isNaN(c) || Float.isNaN(w))
+ continue;
if (pt.x != 0)
addMod("D_S#x;" + atomLabel, fid, P3.new3(c, w, pt.x));
if (pt.y != 0)
@@ -2579,25 +2579,4 @@
return m4;
}
-// static {
-// System.out.println(92345678);
-// System.out.println(999999999);
-// System.out.println(Parser.parseFloatStr("-8.6634100000000014E-01")
-// + " " + Float.valueOf(("-8.6634100000000014E-01")));
-// System.out.println(Parser.parseFloatStr("-0.0000000000663415E-01")
-// + " " + Float.valueOf(("-0.0000000000663415E-01")));
-//
-// System.out.println(Parser.parseFloatStr("-0.0000663415E-01")
-// + " " + Float.valueOf(("-0.0000663415E-01")));
-// System.out.println(Parser.parseFloatStr("-0.00663415E-01")
-// + " " + Float.valueOf(("-0.00663415E-01")));
-// System.out.println(Parser.parseFloatStr("-0.00000000663415E-01")
-// + " " + Float.valueOf(("-0.00000000663415E-01")));
-// System.out.println(Parser.parseFloatStr("-0.0663415E-01")
-// + " " + Float.valueOf(("-0.0663415E-01")));
-// System.out.println(Parser.parseFloatStr("-0.663415E-01")
-// + " " + Float.valueOf(("-0.663415E-01")));
-//
-// }
-
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-12 02:02:51 UTC (rev 18551)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-12 20:16:55 UTC (rev 18552)
@@ -40,6 +40,7 @@
import org.jmol.util.ModulationSet;
import org.jmol.util.P3;
import org.jmol.util.SB;
+import org.jmol.util.Tensor;
import org.jmol.util.TextFormat;
import org.jmol.util.V3;
@@ -85,6 +86,8 @@
modAxes = getFilter("MODAXES=");
modVib = checkFilterKey("MODVIB"); // then use MODULATION ON to see
modulation
modAverage = checkFilterKey("MODAVE");
+ if (!modVib && !modAverage)
+ addJmolScript("modulation on");
checkSpecial = !checkFilterKey("NOSPECIAL");
atomSetCollection.setCheckSpecial(checkSpecial);
allowRotations = !checkFilterKey("NOSYM");
@@ -206,7 +209,8 @@
params = getMod(atomName.substring(pt_ + 2));
atomName = atomName.substring(0, pt_);
}
- System.out.println(key + " " + params);
+ if (Logger.debuggingHigh)
+ Logger.debug("SetModulation: " + key + " " + params);
int type = key.charAt(0);
pt_ = key.indexOf("#") + 1;
String utens = null;
@@ -282,7 +286,8 @@
iop = 0;
// now set to
int mdim = 0; // just the first row -- assuming d=1 here
- //System.out.println("=========MR i=" + a.index + " " + a.atomName + " " +
a + " " + a.occupancy);
+ if (Logger.debuggingHigh)
+ Logger.debug("setModulation: i=" + a.index + " " + a.atomName + " xyz="
+ a + " occ=" + a.occupancy);
if (iop != iopLast) {
symmetry.getMod456Row(iop, mdim, f4);
//System.out.println("mdim=" + mdim + " op=" + (iop + 1) + " " +
symmetry.getSpaceGroupOperation(iop) + " " + symmetry.getSpaceGroupXyz(iop,
false));
@@ -307,11 +312,22 @@
if (ms.htValues != null) {
// Uiso or Uij. We add the displacements, create the tensor, then rotate
it,
// replacing the tensor already present for that atom.
- System.out.println("U1: " + a.index + " " + a.atomName + " " + a + " " +
Escape.eAF(a.anisoBorU));
+ if (Logger.debuggingHigh) {
+ Logger.debug("setModulation Uij(initial)=" + Escape.eAF(a.anisoBorU));
+ Logger.debug("setModulation tensor=" +
Escape.e(a.tensors.get(0).getInfo("all")));
+ }
for (Entry<String, Float>e : ms.htValues.entrySet())
addUStr(a, e.getKey(), e.getValue().floatValue());
- atomSetCollection.addRotatedTensor(a, symmetry.getTensor(a.anisoBorU),
iop, true);
- System.out.println("U2: " + a.index + " " + a.atomName + " " + a + " " +
Escape.eAF(a.anisoBorU) + "\n");
+
+ if (a.tensors != null)
+ a.tensors.get(0).isUnmodulated = true;
+ Tensor t = atomSetCollection.addRotatedTensor(a,
symmetry.getTensor(a.anisoBorU), iop, false);
+ t.isModulated = true;
+ System.out.println("Uij modulation for " + a.atomName);
+ if (Logger.debuggingHigh) {
+ Logger.debug("setModulation Uij(final)=" + Escape.eAF(a.anisoBorU) +
"\n");
+ Logger.debug("setModulation tensor=" +
a.tensors.get(0).getInfo("all"));
+ }
}
// set property_modT to be Math.floor (q.r/|q|) -- really only for d=1
@@ -323,10 +339,10 @@
sb.append(((int) t) + "\n");
}
// displace the atom and reverse the vector only if not filter "MODVIB"
- if (!modVib) {
- a.add(ms);
- ms.setModT(true, Integer.MAX_VALUE);
- }
+// if (!modVib) {
+ // a.add(ms);
+ // ms.setModT(true, Integer.MAX_VALUE);
+ // }
symmetry.toCartesian(ms, true);
//System.out.println("a.vib(xyz)=" + a.vib);
}
@@ -344,7 +360,8 @@
private void addUStr(Atom atom, String id, float val) {
int i = U_LIST.indexOf(id) / 3;
- System.out.println("adding " + id + " " + i + " " + val + " to " +
atom.anisoBorU[i]);
+ if (Logger.debuggingHigh)
+ Logger.debug("MOD RDR adding " + id + " " + i + " " + val + " to " +
atom.anisoBorU[i]);
setU(atom, i, val + atom.anisoBorU[i]);
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
2013-08-12 02:02:51 UTC (rev 18551)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
2013-08-12 20:16:55 UTC (rev 18552)
@@ -570,7 +570,7 @@
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,
false);
+ atom.addTensor(Tensor.getTensorFromAsymmetricTensor(a, "charge",
atom.atomName + " " + line0), null, false);
if (!haveCharges)
appendLoadNote("Ellipsoids set \"charge\": Born Effective Charges");
haveCharges = true;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2013-08-12 02:02:51 UTC (rev 18551)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2013-08-12 20:16:55 UTC (rev 18552)
@@ -1022,7 +1022,7 @@
atoms[index].addTensor(Tensor.getTensorFromEigenVectors(directLatticeVectors,
new float[] {parseFloatStr(tokens[1]),
parseFloatStr(tokens[3]),
- parseFloatStr(tokens[5]) }, "unknown"), null, false);
+ parseFloatStr(tokens[5]) }, "unknown", atoms[index].atomName),
null, false);
readLine();
}
return true;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagresReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagresReader.java
2013-08-12 02:02:51 UTC (rev 18551)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/MagresReader.java
2013-08-12 20:16:55 UTC (rev 18552)
@@ -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, false);
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-08-12 02:02:51 UTC
(rev 18551)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-08-12 20:16:55 UTC
(rev 18552)
@@ -24,6 +24,7 @@
package org.jmol.adapter.smarter;
+import org.jmol.util.ArrayUtil;
import org.jmol.util.BS;
import org.jmol.util.JmolList;
import org.jmol.util.P3;
@@ -55,14 +56,15 @@
public float[] anisoBorU; //[6] = 1 for U, 0 for B; [7] = bFactor
public JmolList<Tensor> tensors;
- public void addTensor(Tensor tensor, String type, boolean reset) {
+ public Tensor addTensor(Tensor tensor, String type, boolean reset) {
if (tensor == null)
- return;
+ return null;
if (reset || tensors == null)
tensors = new JmolList<Tensor>();
tensors.addLast(tensor);
if (type != null)
tensor.setType(type);
+ return tensor;
}
@@ -80,7 +82,14 @@
public Atom getClone() throws CloneNotSupportedException {
// note that anisoBorU and ellipsoid are not copied
// we consider them "final" in a sense
- return (Atom)clone();
+ Atom a = (Atom)clone();
+ if (vib != null)
+ a.vib = V3.newV(a.vib);
+ if (anisoBorU != null)
+ a.anisoBorU = ArrayUtil.arrayCopyF(anisoBorU, -1);
+
+
+ return a;
}
public String getElementSymbol() {
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-08-12 02:02:51 UTC (rev 18551)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-08-12 20:16:55 UTC (rev 18552)
@@ -1160,6 +1160,10 @@
rmaxz = -Float.MAX_VALUE;
}
// always do the 555 cell first
+
+ // incommensurate symmetry can have lattice centering, reulting in
+ // duplication of operators.
+ checkAll = checkSpecial && symmetry.hasLatticeCentering();
Matrix4f op = symmetry.getSpaceGroupOperation(0);
if (doPackUnitCell)
ptOffset.set(0, 0, 0);
@@ -1208,7 +1212,6 @@
}
// now apply all the translations
-
iCell = 0;
for (int tx = minXYZ.x; tx < maxXYZ.x; tx++)
for (int ty = minXYZ.y; ty < maxXYZ.y; ty++)
@@ -1259,6 +1262,7 @@
private int bondIndex0;
private boolean applySymmetryToBonds = false;
private boolean checkSpecial = true;
+ private boolean checkAll = false;
public void setCheckSpecial(boolean TF) {
checkSpecial = TF;
@@ -1267,8 +1271,9 @@
private P3 ptTemp;
private Matrix3f mTemp;
- private int symmetryAddAtoms(int iAtomFirst, int noSymmetryCount, int transX,
- int transY, int transZ, int baseCount, int pt,
+ private int symmetryAddAtoms(int iAtomFirst, int noSymmetryCount,
+ int transX, int transY, int transZ,
+ int baseCount, int pt,
int iCellOpPt, P3[] cartesians) throws
Exception {
boolean isBaseCell = (baseCount == 0);
boolean addBonds = (bondCount0 > bondIndex0 && applySymmetryToBonds);
@@ -1324,7 +1329,7 @@
transZ);
Atom special = null;
P3 cartesian = P3.newP(ptAtom);
- symmetry.toCartesian(cartesian, false);
+ symmetry. toCartesian(cartesian, false);
if (doPackUnitCell) {
symmetry.toUnitCell(cartesian, ptOffset);
ptAtom.setT(cartesian);
@@ -1343,11 +1348,14 @@
float minDist2 = Float.MAX_VALUE;
if (checkSymmetryRange && !isInSymmetryRange(cartesian))
continue;
- for (int j = pt0; --j >= 0;) {
+ int j0 = (checkAll ? atomCount : pt0);
+ for (int j = j0; --j >= 0;) {
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;
@@ -1403,14 +1411,14 @@
return pt;
}
- public void addRotatedTensor(Atom a, Tensor t, int iSym, boolean reset) {
+ public Tensor addRotatedTensor(Atom a, Tensor t, int iSym, boolean reset) {
if (ptTemp == null) {
ptTemp = new P3();
mTemp = new Matrix3f();
}
- a.addTensor(Tensor.getTensorFromEigenVectors(symmetry
+ return a.addTensor(Tensor.getTensorFromEigenVectors(symmetry
.rotateAxes(iSym, t.eigenVectors, ptTemp, mTemp),
- t.eigenValues, t.type), null, reset);
+ t.eigenValues, t.isIsotropic ? "iso" : t.type, t.id), null, reset);
}
public void applySymmetryBio(JmolList<Matrix4f> biomts, float[]
notionalUnitCell, boolean applySymmetryToBonds, String filter) {
@@ -1481,7 +1489,6 @@
mat.m23 /= notionalUnitCell[2];
if (symmetry != null && i > 0)
symmetry.addSpaceGroupOperationM(mat);
- //System.out.println("biomt " + i + " " + atomCount);
}
int noSymmetryCount = atomMax - iAtomFirst;
setAtomSetAuxiliaryInfo("presymmetryAtomIndex",
Integer.valueOf(iAtomFirst));
@@ -1965,7 +1972,6 @@
for (int i = 0; i < bondCount; i++) {
info[i] = new String[] { atoms[bonds[i].atomIndex1].atomName,
atoms[bonds[i].atomIndex2].atomName, "" + bonds[i].order };
- //System.out.println("testing asc getBondList " + info[i][0] + " " +
info[i][1] + " " + info[i][2]);
}
return info;
}
Modified: trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2013-08-12 02:02:51 UTC
(rev 18551)
+++ trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2013-08-12 20:16:55 UTC
(rev 18552)
@@ -176,5 +176,7 @@
public void unitize(P3 ptFrac);
public void addLatticeVectors(JmolList<float[]> lattvecs);
+
+ public boolean hasLatticeCentering();
}
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2013-08-12 02:02:51 UTC (rev
18551)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2013-08-12 20:16:55 UTC (rev
18552)
@@ -291,7 +291,14 @@
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));
+ if (tensors == null)
+ return 0;
+ Tensor t = tensors[0];
+ if (t == null || t.iType != Tensor.TYPE_ADP)
+ return 0;
+ if (group.chain.model.modelSet.isModulated(index) && t.isUnmodulated)
+ t = tensors[1];
+ return t.getFactoredValue(isMax ? 2 : 1);
}
public Tensor[] getTensors() {
@@ -723,7 +730,7 @@
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: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-08-12
02:02:51 UTC (rev 18551)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-08-12
20:16:55 UTC (rev 18552)
@@ -105,6 +105,8 @@
ionicRadii = mergeModelSet.ionicRadii;
partialCharges = mergeModelSet.partialCharges;
atomTensors = mergeModelSet.atomTensors;
+ atomTensorList = mergeModelSet.atomTensorList;
+ bsModulated = mergeModelSet.bsModulated;
setHaveStraightness(false);
surfaceDistance100s = null;
}
@@ -2508,6 +2510,12 @@
return bs;
}
+ BS bsModulated;
+
+ public boolean isModulated(int i) {
+ return bsModulated != null && bsModulated.get(i);
+ }
+
protected void deleteModelAtoms(int firstAtomIndex, int nAtoms, BS bsAtoms) {
// all atoms in the model are being deleted here
atoms = (Atom[]) ArrayUtil.deleteElements(atoms, firstAtomIndex, nAtoms);
@@ -2516,6 +2524,10 @@
atoms[j].index = j;
atoms[j].modelIndex--;
}
+ // fix modulation and tensors
+ if (bsModulated != null)
+ BSUtil.deleteBits(bsModulated, bsAtoms);
+
deleteAtomTensors(bsAtoms);
atomNames = (String[]) ArrayUtil.deleteElements(atomNames, firstAtomIndex,
nAtoms);
@@ -2631,12 +2643,14 @@
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];
+ if (tensors != null && type != null) {
+ type = type.toLowerCase();
+ for (int j = 0; j < tensors.length; j++) {
+ Tensor t = tensors[j];
+ if (t != null && (type.equals(t.type) || type.equals(t.altType)))
+ return t;
+ }
+ }
return null;
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-08-12
02:02:51 UTC (rev 18551)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-08-12
20:16:55 UTC (rev 18552)
@@ -2876,7 +2876,7 @@
unitCells = (SymmetryInterface[]) ArrayUtil.deleteElements(unitCells,
modelIndex, 1);
}
-
+
// correct stateScripts, particularly CONNECT scripts
for (int i = stateScripts.size(); --i >= 0;) {
if (!stateScripts.get(i).deleteAtoms(modelIndex, bsBonds, bsAtoms)) {
@@ -3120,7 +3120,7 @@
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;) {
@@ -3152,7 +3152,7 @@
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);
@@ -3458,6 +3458,8 @@
}
public void setModulation(BS bs, boolean isOn, int t) {
+ if (bsModulated == null)
+ bsModulated = new BS();
//System.out.println("setModulation " + isOn + " " + t);
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
Vibration v = getVibration(i, false);
@@ -3491,6 +3493,7 @@
a.sub(ms);
break;
}
+ bsModulated.setBitTo(i, ms.enabled);
//System.out.println(a.x + " " + a.y + " " + a.z + " ms is " + ms + " "
+ ms.enabled + " " + ms.t);
}
}
Modified: trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java
===================================================================
--- trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java 2013-08-12 02:02:51 UTC
(rev 18551)
+++ trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java 2013-08-12 20:16:55 UTC
(rev 18552)
@@ -1,4 +1,4 @@
- /* $RCSfile$
+/* $RCSfile$
* $Author: hansonr $
* $Date: 2006-05-13 19:17:06 -0500 (Sat, 13 May 2006) $
* $Revision: 5114 $
@@ -100,8 +100,8 @@
*/
@SuppressWarnings("unchecked")
private JmolList<Tensor> getInteractionTensorList(String type, BS bsA) {
- type = type.toLowerCase();
-
+ 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);
@@ -114,7 +114,7 @@
int n = tensors.size();
for (int j = 0; j < n; j++) {
Tensor t = tensors.get(j);
- if (t.type.equals(type) && t.isSelected(bs1, iAtom))
+ if (type == null || t.type.equals(type) && t.isSelected(bs1, iAtom))
list.addLast(t);
}
}
@@ -391,10 +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))
@@ -406,7 +407,9 @@
.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);
int n = (list == null ? 0 : list.size());
@@ -419,9 +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));
Modified: trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
2013-08-12 02:02:51 UTC (rev 18551)
+++ trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
2013-08-12 20:16:55 UTC (rev 18552)
@@ -197,6 +197,7 @@
boolean needTranslucent = false;
Iterator<Ellipsoid> e = ht.values().iterator();
Atom atom = null;
+ System.out.println("ellipsoidrend");
while (e.hasNext()) {
Ellipsoid ellipsoid = e.next();
if (!ellipsoid.visible)
@@ -213,6 +214,7 @@
needTranslucent = true;
continue;
}
+ System.out.println(ellipsoid.tensor.getInfo("all"));
viewer.transformPtScr(ellipsoid.center, s0);
renderOne(ellipsoid);
}
Modified: trunk/Jmol/src/org/jmol/script/SV.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/SV.java 2013-08-12 02:02:51 UTC (rev
18551)
+++ trunk/Jmol/src/org/jmol/script/SV.java 2013-08-12 20:16:55 UTC (rev
18552)
@@ -548,17 +548,17 @@
case bitset:
return iValue(x);
case point3f:
- return ((P3) x.value).distance(pt0);
+ return ((P3) x.value).length();
case point4f:
return Measure.distanceToPlane((P4) x.value, pt0);
case matrix3f:
P3 pt = new P3();
((Matrix3f) x.value).transform(pt);
- return pt.distance(pt0);
+ return pt.length();
case matrix4f:
P3 pt1 = new P3();
((Matrix4f) x.value).transform(pt1);
- return pt1.distance(pt0);
+ return pt1.length();
default:
return 0;
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-08-12 02:02:51 UTC
(rev 18551)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-08-12 20:16:55 UTC
(rev 18552)
@@ -1388,7 +1388,6 @@
// preliminarty checks we only want to do once:
- P3 zero = (minmaxtype == T.allfloat ? new P3() : null);
P3 pt = (isPt || !isAtoms ? new P3() : null);
if (isExplicitlyAll || isString && !haveIndex
&& minmaxtype != T.allfloat && minmaxtype != T.min)
@@ -1738,7 +1737,7 @@
fout[i] = Parser.parseFloatStr((String) v);
break;
case 3:
- fout[i] = ((P3) v).distance(zero);
+ fout[i] = ((P3) v).length();
break;
}
}
@@ -11284,7 +11283,7 @@
break;
case T.set:
sm.loadShape(JC.SHAPE_ELLIPSOIDS);
- setShapeProperty(JC.SHAPE_ELLIPSOIDS, "select", stringParameter(2));
+ setShapeProperty(JC.SHAPE_ELLIPSOIDS, "select", parameterAsString(2));
i = iToken;
checkMore = true;
isSet = true;
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-08-12
02:02:51 UTC (rev 18551)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-08-12
20:16:55 UTC (rev 18552)
@@ -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: trunk/Jmol/src/org/jmol/shapespecial/Ellipsoid.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Ellipsoid.java 2013-08-12 02:02:51 UTC
(rev 18551)
+++ trunk/Jmol/src/org/jmol/shapespecial/Ellipsoid.java 2013-08-12 20:16:55 UTC
(rev 18552)
@@ -128,7 +128,7 @@
protected void setEquation(double[] coef) {
isValid = false;
- tensor = Tensor.getTensorFromThermalEquation(coef);
+ tensor = Tensor.getTensorFromThermalEquation(coef, null);
validate(true);
}
Modified: trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2013-08-12
02:02:51 UTC (rev 18551)
+++ trunk/Jmol/src/org/jmol/shapespecial/Ellipsoids.java 2013-08-12
20:16:55 UTC (rev 18552)
@@ -216,9 +216,13 @@
bs = selectedAtoms;
if (isOn)
setSize(Integer.MAX_VALUE, bs);
- for (Ellipsoid e : atomEllipsoids.values())
- if (e.tensor.type.equals(typeSelected) && e.tensor.isSelected(bs, -1))
+ for (Ellipsoid e : atomEllipsoids.values()) {
+ Tensor t = e.tensor;
+ if ((t.type.equals(typeSelected) || typeSelected.equals(t.altType))
+ && t.isSelected(bs, -1)) {
e.isOn = isOn;
+ }
+ }
return;
}
@@ -235,7 +239,7 @@
e.options = options;
return;
}
-
+
if ("color" == propertyName) {
short colix = C.getColixO(value);
byte pid = EnumPalette.pidOf(value);
@@ -389,11 +393,19 @@
Iterator<Ellipsoid> e = ellipsoids.values().iterator();
while (e.hasNext()) {
Ellipsoid ellipsoid = e.next();
- ellipsoid.visible = ellipsoid.isValid && ellipsoid.isOn
- && (ellipsoid.modelIndex < 0 || bs.get(ellipsoid.modelIndex));
- if (ellipsoid.tensor.atomIndex1 >= 0)
-
atoms[ellipsoid.tensor.atomIndex1].setShapeVisibility(myVisibilityFlag, true);
-
+ Tensor t = ellipsoid.tensor;
+ boolean isOK = true;
+ if (t.atomIndex1 >= 0) {
+ if (t.iType == Tensor.TYPE_ADP) {
+ boolean isModTensor = t.isModulated;
+ boolean isUnmodTensor = t.isUnmodulated;
+ boolean isModAtom = modelSet.isModulated(t.atomIndex1);
+ isOK =(!isModTensor && !isUnmodTensor || isModTensor == isModAtom);
+ }
+ atoms[t.atomIndex1].setShapeVisibility(myVisibilityFlag, true);
+ }
+ ellipsoid.visible = isOK && ellipsoid.isValid && ellipsoid.isOn
+ && (ellipsoid.modelIndex < 0 || bs.get(ellipsoid.modelIndex));
}
}
Modified: trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2013-08-12 02:02:51 UTC
(rev 18551)
+++ trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2013-08-12 20:16:55 UTC
(rev 18552)
@@ -73,7 +73,10 @@
class SpaceGroup {
+ private static String[] canonicalSeitzList;
+
int index;
+
String name = "unknown!";
String hallSymbol;
//String schoenfliesSymbol; //parsed but not read
@@ -96,9 +99,18 @@
int latticeParameter;
char latticeCode = '\0';
SymmetryOperation[] operations;
+ SymmetryOperation[] finalOperations;
int operationCount;
+ boolean hasLatticeCentering;
+ Map<String, Integer> xyzList = new Hashtable<String, Integer>();
+
+ private int modulationDimension;
+
boolean doNormalize = true;
+
+
+
static SpaceGroup getNull() {
getSpaceGroups();
return new SpaceGroup(null);
@@ -142,8 +154,6 @@
return addOperation(xyz, opId);
}
- SymmetryOperation[] finalOperations;
-
void setFinalOperations(P3[] atoms, int atomIndex, int count,
boolean doNormalize) {
//from AtomSetCollection.applySymmetry only
@@ -285,9 +295,7 @@
}
///// private methods /////
-
- private static String[] canonicalSeitzList;
-
+
/**
*
* @return either a String or a SpaceGroup, depending on index.
@@ -390,9 +398,6 @@
return sg;
}
- Map<String, Integer> xyzList = new Hashtable<String, Integer>();
- private int modulationDimension;
-
private int addOperation(String xyz0, int opId) {
if (xyz0 == null || xyz0.length() < 3) {
xyzList = new Hashtable<String, Integer>();
@@ -425,6 +430,8 @@
// ! in character 0 indicates we are using the symop() function and want
to be explicit
if (xyzList.containsKey(xyz))
return xyzList.get(xyz).intValue();
+ if (!hasLatticeCentering &&
xyzList.containsKey(TextFormat.simpleReplace(TextFormat.simpleReplace(xyz,
"+1/2", ""), "+1/2", "")))
+ hasLatticeCentering = true;
xyzList.put(xyz, Integer.valueOf(operationCount));
}
if (xyz != null && !xyz.equals(xyz0))
@@ -1374,6 +1381,7 @@
}
public void addLatticeVectors(JmolList<float[]> lattvecs) {
+ hasLatticeCentering = true;
int nOps = operationCount;
for (int j = 0; j < lattvecs.size(); j++) {
float[] data = lattvecs.get(j);
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2013-08-12 02:02:51 UTC
(rev 18551)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2013-08-12 20:16:55 UTC
(rev 18552)
@@ -652,4 +652,8 @@
spaceGroup.addLatticeVectors(lattvecs);
}
+ public boolean hasLatticeCentering() {
+ return spaceGroup.hasLatticeCentering;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/symmetry/UnitCell.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/UnitCell.java 2013-08-12 02:02:51 UTC
(rev 18551)
+++ trunk/Jmol/src/org/jmol/symmetry/UnitCell.java 2013-08-12 20:16:55 UTC
(rev 18552)
@@ -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;
@@ -302,7 +303,7 @@
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];
@@ -362,7 +363,8 @@
//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: trunk/Jmol/src/org/jmol/util/Logger.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Logger.java 2013-08-12 02:02:51 UTC (rev
18551)
+++ trunk/Jmol/src/org/jmol/util/Logger.java 2013-08-12 20:16:55 UTC (rev
18552)
@@ -84,6 +84,7 @@
public static void setLogger(LoggerInterface logger) {
_logger = logger;
debugging = isActiveLevel(LEVEL_DEBUG) || isActiveLevel(LEVEL_DEBUGHIGH);
+ debuggingHigh = (debugging && _activeLevels[LEVEL_DEBUGHIGH]);
}
/**
@@ -110,6 +111,7 @@
level = LEVEL_MAX - 1;
_activeLevels[level] = active;
debugging = isActiveLevel(LEVEL_DEBUG) || isActiveLevel(LEVEL_DEBUGHIGH);
+ debuggingHigh = (debugging && _activeLevels[LEVEL_DEBUGHIGH]);
}
/**
Modified: trunk/Jmol/src/org/jmol/util/Modulation.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-12 02:02:51 UTC
(rev 18551)
+++ trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-12 20:16:55 UTC
(rev 18552)
@@ -134,7 +134,8 @@
v += a1 * Math.cos(theta);
if (a2 != 0)
v += a2 * Math.sin(theta);
- //System.out.println("MOD v " + v + " a1 a2 " + a1 + " " + a2 + " / " +
theta + " " + ms.t);
+ if (Logger.debuggingHigh)
+ Logger.debug("MOD v " + v + " a1 a2 " + a1 + " " + a2 + " / " + theta
+ " " + ms.t);
break;
case TYPE_OCC_CRENEL:
Modified: trunk/Jmol/src/org/jmol/util/ModulationSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-12 02:02:51 UTC
(rev 18551)
+++ trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-12 20:16:55 UTC
(rev 18552)
@@ -46,7 +46,8 @@
if (htValues == null)
htValues = new Hashtable<String, Float>();
Float f = htValues.get(utens);
- System.out.println("MOD " + id + " n=" + n + " utens=" + utens + " f=" + f
+ " v="+ v);
+ if (Logger.debuggingHigh)
+ Logger.debug("MODSET " + id + " n=" + n + " utens=" + utens + " f=" + f
+ " v="+ v);
if(f != null)
v += f.floatValue();
htValues.put(utens, Float.valueOf(v));
Modified: trunk/Jmol/src/org/jmol/util/Tensor.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Tensor.java 2013-08-12 02:02:51 UTC (rev
18551)
+++ trunk/Jmol/src/org/jmol/util/Tensor.java 2013-08-12 20:16:55 UTC (rev
18552)
@@ -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;
@@ -114,13 +116,16 @@
public int modelIndex;
public int atomIndex1 = -1;
public int atomIndex2 = -1;
+ public boolean isModulated;
+ public boolean isUnmodulated;
private static final String infoList =
";............." + ";eigenvalues.." + ";eigenvectors."
+ ";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 +142,11 @@
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 +203,9 @@
return this.toString();
case 14:
return type;
+
+ case 15:
+ return id;
}
}
@@ -222,6 +233,7 @@
t.modelIndex = t0.modelIndex;
t.atomIndex1 = t0.atomIndex1;
t.atomIndex2 = t0.atomIndex2;
+ t.id = t0.id;
return t;
}
@@ -237,9 +249,10 @@
*
* @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 +297,10 @@
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 +310,18 @@
* @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 +355,14 @@
* (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 +423,17 @@
* @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: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-12 02:02:51 UTC
(rev 18551)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-12 20:16:55 UTC
(rev 18552)
@@ -11,8 +11,17 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.3.4_dev_2013.08.11"
+___JmolVersion="13.3.4_dev_2013.08.12"
+new feature: incommensurate modulation of ADPs.
+
+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: Jsmol menu and console broken in 2013.08.07 when jQuery calls were
all moved into JSmolCore.js
bug fix: float parser broken in dev_2013.08.07
Modified: trunk/Jmol/src/org/openscience/jmol/app/surfacetool/SurfaceTool.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/surfacetool/SurfaceTool.java
2013-08-12 02:02:51 UTC (rev 18551)
+++ trunk/Jmol/src/org/openscience/jmol/app/surfacetool/SurfaceTool.java
2013-08-12 20:16:55 UTC (rev 18552)
@@ -150,7 +150,7 @@
//set positionMin to minimum of BBoxCornerMin.x .y or .z or if all are
//negative -1* distance from origin. PositionMax similarly.
if (negCorner.x < 0 && negCorner.y < 0 && negCorner.z < 0) {
- positionMin = -1 * negCorner.distance(P3.new3(0, 0, 0));
+ positionMin = -1 * negCorner.length();
} else {
positionMin = Math.min(negCorner.x, negCorner.y);
positionMin = Math.min(negCorner.z, positionMin);
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