Revision: 18612
http://sourceforge.net/p/jmol/code/18612
Author: hansonr
Date: 2013-08-21 22:41:14 +0000 (Wed, 21 Aug 2013)
Log Message:
-----------
Incommensurate modulation work up to subsystems.
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/JanaReader.java
trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/util/Matrix3f.java
trunk/Jmol/src/org/jmol/util/Modulation.java
trunk/Jmol/src/org/jmol/util/ModulationSet.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-21
14:46:32 UTC (rev 18611)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-21
22:41:14 UTC (rev 18612)
@@ -1036,7 +1036,7 @@
break;
case OCCUPANCY:
float floatOccupancy = parseFloatStr(field);
- if (Float.isNaN(floatOccupancy))
+ if (!Float.isNaN(floatOccupancy))
atom.foccupancy = floatOccupancy;
break;
case B_ISO:
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-21 14:46:32 UTC (rev 18611)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-21 22:41:14 UTC (rev 18612)
@@ -164,8 +164,10 @@
}
protected void finalizeModulation() {
- if (incommensurate && !modVib)
- addJmolScript("modulation on");
+ if (!incommensurate)
+ return;
+ if (!modVib)
+ addJmolScript("modulation on" + (haveOccupancy ? ";display occupancy >
0.5" : ""));
}
private String suffix;
@@ -173,8 +175,9 @@
return htModulation.get(key + suffix);
}
- private P3[] q123;
+ private Matrix3f q123;
private double[] qlen;
+ private boolean haveOccupancy;
private void setModulationForStructure(int iModel) {
suffix = "@" + iModel;
@@ -182,19 +185,19 @@
if (htModulation.containsKey("X_" + suffix))
return;
htModulation.put("X_" +suffix, new P3());
- q123 = new P3[3];
+ q123 = new Matrix3f();
qlen = new double[modDim];
for (int i = 0; i < modDim; i++) {
- q123[i] = getMod("W_" + (i + 1));
- if (q123[i] == null) {
+ P3 pt = getMod("W_" + (i + 1));
+ if (pt == null) {
Logger.info("Not enough cell wave vectors for d=" + modDim);
return;
}
- qlen[i] = q123[i].length();
+ if (i == 0)
+ q1 = P3.newP(pt);
+ q123.setRowV(i, pt);
+ qlen[i] = pt.length();
}
- for (int i = modDim; i < 3; i++)
- q123[i] = new P3();
- q1 = q123[0];
q1Norm = V3.new3(q1.x == 0 ? 0 : 1, q1.y == 0 ? 0 : 1, q1.z == 0 ? 0 : 1);
P3 qlist100 = P3.new3(1, 0, 0);
P3 pt;
@@ -206,8 +209,7 @@
pt = e.getValue();
switch (key.charAt(0)) {
case 'O':
- if (!modVib && bsAtoms == null)
- bsAtoms = atomSetCollection.bsAtoms = BSUtil.newBitSet2(0, n);
+ haveOccupancy = true;
//$FALL-THROUGH$
case 'D':
// fix modulus/phase option only for non-special modulations;
@@ -356,25 +358,23 @@
Logger.debug("setModulation iop = " + iop + " "
+ symmetry.getSpaceGroupXyz(iop, false) + " " + a.bsSymmetry);
}
-
+ Matrix4f q123w = Matrix4f.newMV(q123, new V3());
+ setSubsystemMatrix(a.atomName, q123w);
ModulationSet ms = new ModulationSet(a.index + " " + a.atomName,
- P3.newP(a), a.foccupancy / 10000f, modDim, list, gammaE, gammaIS,
q123, qlen);
+ P3.newP(a), a.foccupancy, modDim, list, gammaE, gammaIS, q123w, qlen);
a.vib = ms;
ms.calculate();
- float occ = ms.vOcc;
- if (!Float.isNaN(occ)) {
- if (modVib && !Float.isNaN(ms.vOcc0)) {
- a.foccupancy = Math.min(1, Math.max(0, ms.vOcc0 + occ));
- if (a.foccupancy < 0)
- a.foccupancy = 0;
-
- } else if (occ < 0.5f) {
- a.foccupancy = 0;
- if (bsAtoms != null)
- bsAtoms.clear(a.index);
- } else if (occ >= 0.5f) {
- a.foccupancy = 1;
- }
+ if (!Float.isNaN(ms.vOcc)) {
+ a.foccupancy = Math.min(1, Math.max(0, ms.vOcc0 + ms.vOcc));
+// if (!modVib) {
+// if (occ < 0.5f) {
+// a.foccupancy = 0;
+// if (bsAtoms != null)
+// bsAtoms.clear(a.index);
+// } else if (occ >= 0.5f) {
+// a.foccupancy = 1;
+// }
+// }
}
if (ms.htUij != null) {
// Uiso or Uij. We add the displacements, create the tensor, then rotate
it,
@@ -416,6 +416,16 @@
//System.out.println("a.vib(xyz)=" + a.vib);
}
+ private void setSubsystemMatrix(String atomName, Matrix4f q123w) {
+ Object o;
+ if (true || htSubsystems == null || (o = htSubsystems.get(";" + atomName))
== null)
+ return;
+// not sure what to do yet.
+ String subcode = (String) o;
+ Matrix4f wmatrix = (Matrix4f) htSubsystems.get(subcode);
+ q123w.mulM4(wmatrix);
+ }
+
protected void addSubsystem(String code, Matrix4f m4, String atomName) {
if (htSubsystems == null)
htSubsystems = new Hashtable<String, Object>();
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-21 14:46:32 UTC (rev 18611)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-21 22:41:14 UTC (rev 18612)
@@ -24,6 +24,8 @@
package org.jmol.adapter.readers.xtal;
import java.io.BufferedReader;
+import java.util.Hashtable;
+import java.util.Map;
import org.jmol.adapter.readers.cif.ModulationReader;
@@ -32,6 +34,7 @@
import org.jmol.util.BS;
import org.jmol.util.JmolList;
import org.jmol.util.Logger;
+import org.jmol.util.Matrix4f;
import org.jmol.util.P3;
import org.jmol.util.TextFormat;
@@ -43,17 +46,17 @@
public class JanaReader extends ModulationReader {
private JmolList<float[]> lattvecs;
+ private int thisSub;
@Override
public void initializeReader() throws Exception {
setFractionalCoordinates(true);
initializeModulation();
atomSetCollection.newAtomSet();
- forcePacked = true; // need site occupancies anyway
}
- final static String records = "tit cell ndim qi lat sym spg end";
- // 0 5 10 15 20 25 30 35
+ final static String records = "tit cell ndim qi lat sym spg end wma";
+ // 0 5 10 15 20 25 30 35 40
final static int TITLE = 0;
final static int CELL = 5;
final static int NDIM = 10;
@@ -62,6 +65,7 @@
final static int SYM = 25;
final static int SPG = 30;
final static int END = 35;
+ final static int WMATRIX = 40;
// Version Jana2006
// title
@@ -114,6 +118,18 @@
case END:
continuing = false;
break;
+ case WMATRIX:
+ Matrix4f m = new Matrix4f();
+ if (thisSub++ == 0) {
+ m.setIdentity();
+ addSubsystem("1", m, null);
+ thisSub++;
+ m = new Matrix4f();
+ }
+ float[] data = new float[16];
+ fillFloatArray(null, 0, data);
+ m.setA(data, 0);
+ addSubsystem("" + thisSub, m, null);
}
return true;
}
@@ -229,16 +245,27 @@
.getLigandModel(id, name, "_file", "----"));
if (readM40Floats(r).startsWith("command"))
readM40WaveVectors(r);
- int nAtoms = (int) floats[0];
- for (int i = 0; i < nAtoms; i++) {
- while (readM40Floats(r).length() == 0 || line.charAt(0) == ' '
- || line.charAt(0) == '-') {
+ BS newSub = getSubSystemList();
+ int iSub = (newSub == null ? 0 : 1);
+ int nAtoms = -1;
+ while (readM40Floats(r) != null) {
+ while (line != null && (line.length() == 0 || line.charAt(0) == ' '
+ || line.charAt(0) == '-')) {
+ readM40Floats(r);
}
-
+ if (line == null)
+ break;
+ nAtoms++;
Atom atom = new Atom();
atom.atomName = line.substring(0, 9).trim();
+ Logger.info(line);
if (!filterAtom(atom, 0))
continue;
+ if (iSub > 0) {
+ if (newSub.get(nAtoms))
+ iSub++;
+ addSubsystem("" + iSub, null, atom.atomName);
+ }
atom.foccupancy = floats[2];
setAtomCoordXYZ(atom, floats[3], floats[4], floats[5]);
atomSetCollection.addAtom(atom);
@@ -314,7 +341,8 @@
} else {
if (haveSpecialUij) {
//TODO
- Logger.error("JanaReader -- not interpreting SpecialUij flag: " +
line);
+ Logger.error("JanaReader -- not interpreting SpecialUij flag: "
+ + line);
} else {
float[][] data = readM40FloatLines(2, 6, r);
for (int k = 0, p = 0; k < 6; k++, p += 3)
@@ -328,6 +356,20 @@
r.close();
}
+ private BS getSubSystemList() {
+ if (htSubsystems == null)
+ return null;
+ BS bs = new BS();
+ String[] tokens = getTokens();
+ for (int i = 0, n = 0; i < tokens.length; i+= 2) {
+ int nAtoms = parseIntStr(tokens[i]);
+ if (nAtoms == 0)
+ break;
+ bs.set(n = n + nAtoms);
+ }
+ return bs;
+ }
+
private void readM40WaveVectors(BufferedReader r) throws Exception {
while (!readM40Floats(r).contains("end"))
if (line.startsWith("wave")) {
@@ -382,7 +424,8 @@
private float[] floats = new float[6];
private String readM40Floats(BufferedReader r) throws Exception {
- line = r.readLine();
+ if ((line = r.readLine()) == null || line.indexOf("-------") >= 0)
+ return (line = null);
if (Logger.debugging)
Logger.debug(line);
int ptLast = line.length() - 10;
@@ -405,15 +448,17 @@
* M40 occupancies are divided by the site multiplicity
*/
private void adjustM40Occupancies() {
- int nOps = atomSetCollection.getSymmetry().getSpaceGroupOperationCount();
- BS bsSite = new BS();
+ Map<String, Integer> htSiteMult = new Hashtable<String, Integer>();
Atom[] atoms = atomSetCollection.getAtoms();
for (int i = atomSetCollection.getAtomCount(); --i >= 0;) {
Atom a = atoms[i];
- bsSite.clearAll();
- bsSite.setBits(0, nOps);
- bsSite.and(a.bsSymmetry);
- a.foccupancy *= bsSite.cardinality();
+ Integer ii = htSiteMult.get(a.atomName);
+ if (ii == null) {
+ System.out.println(a.atomName);
+ htSiteMult.put(a.atomName, ii =
Integer.valueOf(atomSetCollection.getSymmetry().getSiteMultiplicity(a)));
+ System.out.println(a.atomName + " " + ii + " " + a.bsSymmetry + " " +
a.foccupancy);
+ }
+ a.foccupancy *= ii.intValue();
}
}
}
Modified: trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2013-08-21 14:46:32 UTC
(rev 18611)
+++ trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2013-08-21 22:41:14 UTC
(rev 18612)
@@ -178,5 +178,7 @@
public boolean hasLatticeCentering();
public Matrix4f getOperationGammaIS(int iop);
+
+ public int getSiteMultiplicity(P3 a);
}
Modified: trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2013-08-21 14:46:32 UTC
(rev 18611)
+++ trunk/Jmol/src/org/jmol/symmetry/SpaceGroup.java 2013-08-21 22:41:14 UTC
(rev 18612)
@@ -1401,7 +1401,29 @@
}
}
+ public int getSiteMultiplicity(P3 pt, UnitCell unitCell) {
+ int n = finalOperations.length;
+ JmolList<P3> pts = new JmolList<P3>();
+ for (int i = n; --i >= 0;) {
+ P3 pt1 = P3.newP(pt);
+ finalOperations[i].transform(pt1);
+ unitCell.unitize(pt1);
+ for (int j = pts.size(); --j >= 0;) {
+ P3 pt0 = pts.get(j);
+ if (pt1.distanceSquared(pt0) < 0.000001f) {
+ pt1 = null;
+ break;
+ }
+ }
+ if (pt1 != null) {
+ //System.out.println(pt + " to " + pt1 + " by " + i + ": " +
finalOperations[i].xyz);
+ pts.addLast(pt1);
+ }
+ }
+ return n / pts.size();
+ }
+
/* see http://cci.lbl.gov/sginfo/itvb_2001_table_a1427_hall_symbols.html
intl# H-M full HM-abbr HM-short Hall
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2013-08-21 14:46:32 UTC
(rev 18611)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2013-08-21 22:41:14 UTC
(rev 18612)
@@ -653,7 +653,11 @@
return spaceGroup.finalOperations[iop].gammaIS;
}
+ public int getSiteMultiplicity(P3 pt) {
+ return spaceGroup.getSiteMultiplicity(pt,unitCell);
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/util/Matrix3f.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Matrix3f.java 2013-08-21 14:46:32 UTC (rev
18611)
+++ trunk/Jmol/src/org/jmol/util/Matrix3f.java 2013-08-21 22:41:14 UTC (rev
18612)
@@ -279,7 +279,7 @@
* @param v
* the replacement row
*/
- public final void setRowV(int row, V3 v) {
+ public final void setRowV(int row, Tuple3f v) {
if (row == 0) {
m00 = v.x;
m01 = v.y;
Modified: trunk/Jmol/src/org/jmol/util/Modulation.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-21 14:46:32 UTC
(rev 18611)
+++ trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-21 22:41:14 UTC
(rev 18612)
@@ -154,7 +154,7 @@
x -= Math.floor(x);
ms.vOcc = (range(x) ? 1 : 0);
- ms.vOcc0 = Float.NaN; // don't add this in
+ ms.vOcc0 = 0; // absolute
//System.out.println("MOD " + ms.r + " " + ms.delta + " " + ms.epsilon
+ " " + ms.id + " " + ms.v + " l=" + left + " x=" + x4 + " r=" + right);
return;
case TYPE_DISP_SAWTOOTH:
Modified: trunk/Jmol/src/org/jmol/util/ModulationSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-21 14:46:32 UTC
(rev 18611)
+++ trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-21 22:41:14 UTC
(rev 18612)
@@ -46,7 +46,8 @@
*/
public ModulationSet(String id, P3 r, float vocc0, int modDim,
- JmolList<Modulation> mods, Matrix3f gammaE, Matrix4f
gammaIS, P3[] q123, double[] qlen) {
+ JmolList<Modulation> mods, Matrix3f gammaE,
+ Matrix4f gammaIS, Matrix4f q123w, double[] qlen) {
this.id = id;
this.vOcc0 = vocc0;
this.modDim = modDim;
@@ -61,11 +62,13 @@
gammaIS.get(sI);
gammaIinv.invert();
- x456 = V3.new3(q123[0].dot(r), q123[1].dot(r), q123[2].dot(r));
+ x456 = V3.newV(r);
+ Matrix3f m = new Matrix3f();
+ q123w.transform(x456);
x456.sub(sI);
gammaIinv.transform(x456);
if (Logger.debuggingHigh)
- Logger.debug("MODSET create r=" + Escape.eP(r) + " q0=" +
Escape.eP(q123[0])
+ Logger.debug("MODSET create r=" + Escape.eP(r)
+ " si=" + Escape.eP(sI) + " ginv=" +
gammaIinv.toString().replace('\n',' ') + " x4=" + x456.x);
// temporary only - only for d=1:
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