Revision: 20151
http://sourceforge.net/p/jmol/code/20151
Author: hansonr
Date: 2014-12-02 02:52:04 +0000 (Tue, 02 Dec 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.11_2014.12.01"
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:
--------------
trunk/Jmol/src/javajs/util/CifDataParser.java
trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java
trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
trunk/Jmol/src/org/jmol/util/ModulationSet.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/javajs/util/CifDataParser.java
===================================================================
--- trunk/Jmol/src/javajs/util/CifDataParser.java 2014-11-28 22:52:14 UTC
(rev 20150)
+++ trunk/Jmol/src/javajs/util/CifDataParser.java 2014-12-02 02:52:04 UTC
(rev 20151)
@@ -263,7 +263,7 @@
for (int i = 0; i < fieldCount; ++i)
if ((loopData[i] = getNextDataToken()) == null)
return false;
- return true;
+ return (fieldCount > 0);
}
/**
Modified: trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2014-11-28 22:52:14 UTC
(rev 20150)
+++ trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2014-12-02 02:52:04 UTC
(rev 20151)
@@ -112,7 +112,7 @@
boolean doNormalize = true;
- public boolean isBio;
+ boolean isBio;
boolean isBilbao;
@@ -1449,7 +1449,7 @@
"230;oh^10;i a -3 d;-i 4bd 2c 3",
};
- public boolean addLatticeVectors(Lst<float[]> lattvecs) {
+ boolean addLatticeVectors(Lst<float[]> lattvecs) {
if (latticeOp >= 0 || lattvecs.size() == 0)
return false;
int nOps = latticeOp = operationCount;
@@ -1479,7 +1479,7 @@
return true;
}
- public int getSiteMultiplicity(P3 pt, UnitCell unitCell) {
+ int getSiteMultiplicity(P3 pt, UnitCell unitCell) {
int n = finalOperations.length;
Lst<P3> pts = new Lst<P3>();
for (int i = n; --i >= 0;) {
Modified: trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java 2014-11-28 22:52:14 UTC
(rev 20150)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryDesc.java 2014-12-02 02:52:04 UTC
(rev 20151)
@@ -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
@@ -957,12 +957,12 @@
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: trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2014-11-28
22:52:14 UTC (rev 20150)
+++ trunk/Jmol/src/org/jmol/symmetry/SymmetryOperation.java 2014-12-02
02:52:04 UTC (rev 20151)
@@ -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;
@@ -668,13 +668,13 @@
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 +697,47 @@
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 +751,7 @@
* 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: trunk/Jmol/src/org/jmol/util/ModulationSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ModulationSet.java 2014-11-28 22:52:14 UTC
(rev 20150)
+++ trunk/Jmol/src/org/jmol/util/ModulationSet.java 2014-12-02 02:52:04 UTC
(rev 20151)
@@ -61,6 +61,7 @@
private Matrix tFactorInv;
private Matrix rsvs;
+ private float spinOp;
@Override
public float getScale() {
@@ -250,6 +251,8 @@
gammaIinv = rsvs.getSubmatrix(3, 3, d, d).inverse();
Matrix gammaM = rsvs.getSubmatrix(3, 0, d, 3);
Matrix sI = rsvs.getSubmatrix(3, 3 + d, d, 1);
+ spinOp = symmetry.getSpinOp(iop);
+ System.out.println("spinOp " + iop + " " + strop + " " + spinOp);
tau = gammaIinv.mul(sigma.mul(vR0).sub(gammaM.mul(vR00)).sub(sI));
@@ -322,8 +325,11 @@
mods.get(i).apply(this, arI);
// rotate by R3 rotation
gammaE.rotate(this);
- if (mxyz != null)
+ if (mxyz != null){
gammaE.rotate(mxyz);
+ if (spinOp < 0)
+ mxyz.scale(spinOp);
+ }
return this;
}
@@ -451,6 +457,7 @@
modTemp = new ModulationSet();
modTemp.id = id;
modTemp.tau = tau;
+ modTemp.spinOp = spinOp;
modTemp.mods = mods;
modTemp.gammaE = gammaE;
modTemp.modDim = modDim;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-28 22:52:14 UTC
(rev 20150)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-02 02:52:04 UTC
(rev 20151)
@@ -15,8 +15,14 @@
TODO: design and implement sidechain mutation -- MUTATE command ?
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.11_2014.11.28"
+Jmol.___JmolVersion="14.3.11_2014.12.01"
+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
+
+
+JmolVersion="14.3.11_2014.11.28"
+
new feature: readers for ESS input types: CFILE, VFILE, MOPAC, NWChem,
Gaussian, GAMESS, Orca, PQS
-- CFILE and VFILE require CFI:: and VFI:: (or C:: and V::)
-- MOPAC requires MND::
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