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[Jmol-commits] SF.net SVN: jmol:[20158] branches/v14_2/Jmol/src
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From: <ha...@us...> - 2014-12-05 04:21:54
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Revision: 20158
http://sourceforge.net/p/jmol/code/20158
Author: hansonr
Date: 2014-12-05 04:21:46 +0000 (Fri, 05 Dec 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.2.11_2014.12.02"
bug fix: for (x in yUpperCase) fails
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
Modified Paths:
--------------
branches/v14_2/Jmol/src/javajs/util/CifDataParser.java
branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java
branches/v14_2/Jmol/src/org/jmol/symmetry/SymmetryDesc.java
branches/v14_2/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_2/Jmol/src/javajs/util/CifDataParser.java
===================================================================
--- branches/v14_2/Jmol/src/javajs/util/CifDataParser.java 2014-12-05 04:07:05 UTC (rev 20157)
+++ branches/v14_2/Jmol/src/javajs/util/CifDataParser.java 2014-12-05 04:21:46 UTC (rev 20158)
@@ -263,7 +263,7 @@
for (int i = 0; i < fieldCount; ++i)
if ((loopData[i] = getNextDataToken()) == null)
return false;
- return true;
+ return (fieldCount > 0);
}
/**
Modified: branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java 2014-12-05 04:07:05 UTC (rev 20157)
+++ branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java 2014-12-05 04:21:46 UTC (rev 20158)
@@ -8579,9 +8579,9 @@
if (key.startsWith("_"))
invArg();
if (key.indexOf("/") >= 0)
- contextVariables.put(key, t = SV.newI(0));
+ contextVariables.put(key.toLowerCase(), t = SV.newI(0));
else
- t = vwr.g.getOrSetNewVariable(key, true);
+ t = vwr.g.getOrSetNewVariable(key, true);
}
return t;
}
Modified: branches/v14_2/Jmol/src/org/jmol/symmetry/SymmetryDesc.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/symmetry/SymmetryDesc.java 2014-12-05 04:07:05 UTC (rev 20157)
+++ branches/v14_2/Jmol/src/org/jmol/symmetry/SymmetryDesc.java 2014-12-05 04:21:46 UTC (rev 20158)
@@ -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
@@ -484,7 +484,7 @@
draw1
.append(
("// " + op.xyzOriginal + "|" + xyzNew + "|" + info1).replace(
- '\n', ' ')).append("\n").append(drawid).append("* delete");
+ '\n', ' ')).appendC('\n').append(drawid).append("* delete");
// draw the initial frame
@@ -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;
@@ -957,12 +952,12 @@
if (sb.length() > 0)
sb.appendC('\n');
if (prettyMat) {
- sb.append(SymmetryOperation.cleanMatrix((M4) infolist[i][10])).append(
- "\t");
+ SymmetryOperation.getPrettyMatrix(sb, (M4) infolist[i][10]);
+ sb.appendC('\t');
} else if (!labelOnly) {
if (symOp < 0)
- sb.appendI(i + 1).append("\t");
- sb.append((String) infolist[i][0]).append("\t"); //xyz
+ sb.appendI(i + 1).appendC('\t');
+ sb.append((String) infolist[i][0]).appendC('\t'); //xyz
}
sb.append((String) infolist[i][2]); //desc
}
Modified: branches/v14_2/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2014-12-05 04:07:05 UTC (rev 20157)
+++ branches/v14_2/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2014-12-05 04:21:46 UTC (rev 20158)
@@ -77,7 +77,7 @@
private Matrix sigma;
int index;
String subsystemCode;
- public int timeReversal;
+ int timeReversal;
void setSigma(String subsystemCode, Matrix sigma) {
this.subsystemCode = subsystemCode;
@@ -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) {
@@ -668,13 +678,13 @@
return PT.approx(f, 100);
}
- public static void normalizeTranslation(M4 operation) {
+ static void normalizeTranslation(M4 operation) {
operation.m03 = ((int)operation.m03 + 12) % 12;
operation.m13 = ((int)operation.m13 + 12) % 12;
operation.m23 = ((int)operation.m23 + 12) % 12;
}
- public static String getXYZFromRsVs(Matrix rs, Matrix vs, boolean is12ths) {
+ static String getXYZFromRsVs(Matrix rs, Matrix vs, boolean is12ths) {
double[][] ra = rs.getArray();
double[][] va = vs.getArray();
int d = ra.length;
@@ -697,33 +707,47 @@
return (rsvs == null ? super.toString() : super.toString() + " " + rsvs.toString());
}
- float magOp = Float.MAX_VALUE;
+ private boolean unCentered;
boolean isCenteringOp;
- private boolean unCentered;
- public float getSpinOp() {
+
+ private float magOp = Float.MAX_VALUE;
+ /**
+ * Magnetic spin operations have a flag m=1 or m=-1 (m or -m)
+ * that indicates how the vector quantity changes with symmetry.
+ * This we call "timeReversal."
+ *
+ * To apply, timeReversal must be multiplied by the 3x3 determinant, which
+ * is always 1 (standard rotation) or -1 (rotation-inversion). This we store
+ * as magOp.
+ *
+ * For example, a vector perpendicular to a plane of symmetry (det=-1) will be
+ * flipped (m=1), while a vector parallel to that plane will not be flipped (m=-1)
+ *
+ * @return +1, -1, or 0
+ */
+ float getSpinOp() {
if (magOp == Float.MAX_VALUE)
magOp = determinant3() * timeReversal;
//System.out.println("sym op " + index + " " + xyz + " has tr " + timeReversal + " and magop " + magOp);
return magOp;
}
- public void setTimeReversal(int magRev) {
+ void setTimeReversal(int magRev) {
timeReversal = magRev;
if (xyz.indexOf("m") >= 0)
xyz = xyz.substring(0, xyz.indexOf("m"));
xyz += (magRev == 1 ? ",m" : magRev == -1 ? ",-m" : "");
}
- public static String cleanMatrix(M4 m4) {
- SB sb = new SB();
+ static String getPrettyMatrix(SB sb, M4 m4) {
sb.append("[ ");
float[] row = new float[4];
for (int i = 0; i < 3; i++) {
m4.getRow(i, row);
sb.append("[ ")
- .appendI((int)row[0]).append(" ")
- .appendI((int)row[1]).append(" ")
- .appendI((int)row[2]).append(" ");
+ .appendI((int)row[0]).appendC(' ')
+ .appendI((int)row[1]).appendC(' ')
+ .appendI((int)row[2]).appendC(' ');
sb.append(twelfthsOf(row[3]*12)).append(" ]");
}
return sb.append(" ]").toString();
@@ -737,7 +761,7 @@
* TODO
* @return centering
*/
- public V3 setCentering(V3 c, boolean isFinal) {
+ V3 setCentering(V3 c, boolean isFinal) {
if (centering == null && !unCentered) {
if (modDim == 0 && index > 1 && m00 == 1 && m11 == 1 && m22 == 1
&& m01 == 0 && m02 == 0 && m10 == 0 && m12 == 0 && m20 == 0
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-05 04:07:05 UTC (rev 20157)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-05 04:21:46 UTC (rev 20158)
@@ -4,7 +4,7 @@
# THIS IS THE RELEASE BRANCH
# BUG FIXES ONLY, PLEASE
-Jmol.___JmolVersion="14.3.11_2014.12.02"
+Jmol.___JmolVersion="14.2.11_2014.12.02"
bug fix: for (x in yUpperCase) fails
bug fix: draw SYMOP fails for incommensurate space groups
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