Revision: 20153
http://sourceforge.net/p/jmol/code/20153
Author: hansonr
Date: 2014-12-02 13:02:07 +0000 (Tue, 02 Dec 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.11_2014.12.02"
bug fix: draw SYMOP fails for incommensurate space groups
bug fix: incommensurate magnetic CIF reading does not apply magnetic spin
operation to spin modulations
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java
trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java 2014-12-02 03:20:59 UTC
(rev 20152)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java 2014-12-02 13:02:07 UTC
(rev 20153)
@@ -462,8 +462,8 @@
if (haveCentering)
info1 += "|centering " + strCoord(op.centering, op.isBio);
- if (op.timeReversal != 0)
- info1 += "|spin " + (op.timeReversal == 1 ? "m" : "-m");
+ if (op.timeReversal != 0 && op.getSpinOp() == -1)
+ info1 += "|spin flipped";
String cmds = null;
String xyzNew = (op.isBio ? op.xyzOriginal : SymmetryOperation
@@ -762,8 +762,8 @@
}
xyzNew = (op.isBio ? m2.toString() : op.modDim > 0 ? op.xyzOriginal
: SymmetryOperation.getXYZFromMatrix(m2, false, false, false));
- if (op.timeReversal != 0)
- xyzNew += (op.timeReversal == 1 ? ",m" : ",-m");
+ //if (op.timeReversal != 0)
+ //xyzNew += (op.timeReversal == 1 ? ",m" : ",-m");
return new Object[] { xyzNew, op.xyzOriginal, info1, cmds, approx0(ftrans),
approx0(trans), approx0(ipt), approx0(pa1), approx0(ax1),
Integer.valueOf(ang1), m2, vtrans, op.centering };
@@ -846,14 +846,9 @@
if (xyz == null) {
SymmetryOperation[] ops = (SymmetryOperation[]) uc
.getSymmetryOperations();
- if (ops == null || op == 0 || Math.abs(op) > ops.length) {
+ if (ops == null || op == 0 || Math.abs(op) > ops.length)
return (type == T.draw ? "draw ID sym_* delete" : "");
- }
- if (op > 0) {
- xyz = ops[iop = op - 1].xyz;
- } else {
- xyz = ops[iop = -1 - op].xyz;
- }
+ xyz = ops[iop = Math.abs(op) - 1].xyz;
centering = ops[iop].centering;
} else {
iop = op = 0;
Modified: trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2014-12-02
03:20:59 UTC (rev 20152)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2014-12-02
13:02:07 UTC (rev 20153)
@@ -217,11 +217,7 @@
return false;
xyzOriginal = xyz;
xyz = xyz.toLowerCase();
- int n = (modDim + 4) * (modDim + 4);
- this.modDim = modDim;
- if (modDim > 0)
- myLabels = labelsXn;
- linearRotTrans = new float[n];
+ setModDim(modDim);
boolean isReverse = (xyz.startsWith("!"));
if (isReverse)
xyz = xyz.substring(1);
@@ -243,23 +239,30 @@
*
*/
this.xyz = xyz;
- Parser.parseStringInfestedFloatArray(xyz, null, linearRotTrans);
+ Parser.parseStringInfestedFloatArray(xyz, null, linearRotTrans);
return setFromMatrix(null, isReverse);
}
if (xyz.indexOf("[[") == 0) {
- xyz = xyz.replace('[',' ').replace(']',' ').replace(',',' ');
+ xyz = xyz.replace('[', ' ').replace(']', ' ').replace(',', ' ');
Parser.parseStringInfestedFloatArray(xyz, null, linearRotTrans);
- for (int i = 0; i < n; i++) {
- float v = linearRotTrans[i];
- if (Float.isNaN(v))
+ for (int i = linearRotTrans.length; --i >= 0;)
+ if (Float.isNaN(linearRotTrans[i]))
return false;
- }
setMatrix(isReverse);
isFinalized = true;
isBio = (xyz.indexOf("bio") >= 0);
- this.xyz = (isBio ? toString() : getXYZFromMatrix(this, false, false,
false));
+ this.xyz = (isBio ? toString() : getXYZFromMatrix(this, false, false,
+ false));
return true;
}
+ if (modDim == 0 && xyz.indexOf("x4") >= 0) {
+ for (int i = 14; --i >= 4;) {
+ if (xyz.indexOf("x" + i) >= 0) {
+ setModDim(i - 3);
+ break;
+ }
+ }
+ }
if (xyz.endsWith("m")) {
timeReversal = (xyz.indexOf("-m") >= 0 ? -1 : 1);
allowScaling = true;
@@ -277,6 +280,13 @@
return true;
}
+ private void setModDim(int dim) {
+ int n = (dim + 4) * (dim + 4);
+ modDim = dim;
+ if (dim > 0)
+ myLabels = labelsXn;
+ linearRotTrans = new float[n];
+ }
private void setMatrix(boolean isReverse) {
if (linearRotTrans.length > 16) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-02 03:20:59 UTC
(rev 20152)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-02 13:02:07 UTC
(rev 20153)
@@ -17,6 +17,7 @@
Jmol.___JmolVersion="14.3.11_2014.12.01"
+bug fix: draw SYMOP fails for incommensurate space groups
bug fix: incommensurate magnetic CIF reading does not apply magnetic spin
operation to spin modulations
bug fix: CIF reader can cycle infinitely if loop_ keywords are not followed by
any data
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