Revision: 18564
http://sourceforge.net/p/jmol/code/18564
Author: hansonr
Date: 2013-08-14 10:38:00 +0000 (Wed, 14 Aug 2013)
Log Message:
-----------
incommensurate work -- M50/40 file reading
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/render/RepaintManager.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/util/Modulation.java
trunk/Jmol/src/org/jmol/util/ModulationSet.java
trunk/Jmol/src/org/jmol/viewer/AnimationManager.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-14
02:43:07 UTC (rev 18563)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2013-08-14
10:38:00 UTC (rev 18564)
@@ -218,7 +218,7 @@
} else if (key.startsWith("_chemical_formula_sum") ||
key.equals("_chem_comp_formula")) {
processChemicalInfo("formula");
} else if (key.equals("_cell_modulation_dimension") && !modAverage) {
- setModDim(data);
+ setModDim(parseIntStr(data));
} else if (key.startsWith("_cell_")) {
processCellParameter();
} else if (key.startsWith("_symmetry_space_group_name_H-M")
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-14 02:43:07 UTC (rev 18563)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-14 10:38:00 UTC (rev 18564)
@@ -68,7 +68,10 @@
protected boolean modVib;
protected String modAxes;
protected boolean modAverage;
+ protected String modType;
protected boolean checkSpecial = true;
+ protected boolean modDebug;
+
protected int modDim;
protected boolean incommensurate;
protected Atom[] atoms;
@@ -83,7 +86,9 @@
protected void initializeMod() throws Exception {
+ modDebug = checkFilterKey("MODDEBUG");
modAxes = getFilter("MODAXES=");
+ modType = getFilter("MODTYPE="); //ODU
modVib = checkFilterKey("MODVIB"); // then use MODULATION ON to see
modulation
modAverage = checkFilterKey("MODAVE");
if (!modVib && !modAverage)
@@ -93,10 +98,10 @@
allowRotations = !checkFilterKey("NOSYM");
}
- protected void setModDim(String token) {
- modDim = parseIntStr(token);
+ protected void setModDim(int ndim) {
if (modAverage)
return;
+ modDim = ndim;
if (modDim > 1) {
// not ready for dim=2
appendLoadNote("Too high modulation dimension (" + modDim + ") --
reading average structure");
@@ -114,9 +119,19 @@
}
protected void addModulation(Map<String, P3> map, String id, P3 pt, int
iModel) {
+ if (modType != null)
+ switch (id.charAt(0)) {
+ case 'O':
+ case 'D':
+ case 'U':
+ if (modType.indexOf(id.charAt(0)) < 0)
+ return;
+ break;
+ }
if (map == null)
map = htModulation;
- id += "@" + (iModel >= 0 ? iModel :
atomSetCollection.getCurrentAtomSetIndex());
+ id += "@"
+ + (iModel >= 0 ? iModel : atomSetCollection.getCurrentAtomSetIndex());
Logger.info("Adding " + id + " " + pt);
map.put(id, pt);
}
@@ -128,7 +143,11 @@
protected void setModulation() {
if (!incommensurate || htModulation == null)
return;
+ if (modDebug)
+ Logger.debugging = Logger.debuggingHigh = false;
setModulationForStructure(atomSetCollection.getCurrentAtomSetIndex());
+ if (modDebug)
+ Logger.debugging = Logger.debuggingHigh = true;
}
private String suffix;
@@ -255,7 +274,6 @@
atomSetCollection.setAtomSetAtomProperty("modt", sb.toString(), -1);
htAtomMods = null;
}
-
private String checkKey(String key) {
int pt_ = key.indexOf(suffix);
return (pt_ < 0 ? null : key.substring(0, pt_));
@@ -285,53 +303,62 @@
if (iop < 0)
iop = 0;
// now set to
- int mdim = 0; // just the first row -- assuming d=1 here
-
+ int mdim = 0; // just the first row -- assuming d=1 here
+
//if (a.index == 40)
- //Logger.debuggingHigh = Logger.debugging = true;
+ //Logger.debuggingHigh = Logger.debugging = true;
if (Logger.debuggingHigh)
- Logger.debug("setModulation: i=" + a.index + " " + a.atomName + " xyz="
+ a + " occ=" + a.occupancy);
+ 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));
iopLast = iop;
rot = new Matrix3f();
- epsilon = f4[0]; //symmetry.getModParam(iop, 0);
- delta = f4[3] - modT; //symmetry.getModParam(iop, 1);
+ epsilon = f4[0]; //symmetry.getModParam(iop, 0);
+ delta = f4[3] - modT; //symmetry.getModParam(iop, 1);
}
symmetry.getSpaceGroupOperation(iop).getRotationScale(rot);
if (Logger.debugging) {
- Logger.debug("setModulation iop = " + iop + " " +
symmetry.getSpaceGroupXyz(iop, false) + " " + a.bsSymmetry);
+ Logger.debug("setModulation iop = " + iop + " "
+ + symmetry.getSpaceGroupXyz(iop, false) + " " + a.bsSymmetry);
}
ModulationSet ms = new ModulationSet(a.index + " " + a.atomName, list);
a.vib = ms;
ms.epsilon = epsilon;
ms.delta = delta;
ms.r = P3.newP(a);
+ ms.v0 = a.occupancy / 100f;
ms.rot = rot;
ms.calculate();
- if (ms.v < 0.5f) {
+ if (modVib && !Float.isNaN(ms.v0)) {
+ a.occupancy = (int) ((ms.v0 + ms.v) * 100);
+ } else if (ms.v < 0.5f) {
a.occupancy = 0;
- if (bsAtoms != null)
- bsAtoms.clear(a.index);
+ bsAtoms.clear(a.index);
+ } else if (ms.v >= 0.5f) {
+ a.occupancy = 100;
}
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.
if (Logger.debuggingHigh) {
Logger.debug("setModulation Uij(initial)=" + Escape.eAF(a.anisoBorU));
- Logger.debug("setModulation tensor=" +
Escape.e(a.tensors.get(0).getInfo("all")));
+ Logger.debug("setModulation tensor="
+ + Escape.e(a.tensors.get(0).getInfo("all")));
}
- for (Entry<String, Float>e : ms.htValues.entrySet())
+ for (Entry<String, Float> e : ms.htValues.entrySet())
addUStr(a, e.getKey(), e.getValue().floatValue());
-
+
if (a.tensors != null)
a.tensors.get(0).isUnmodulated = true;
- Tensor t = atomSetCollection.addRotatedTensor(a,
symmetry.getTensor(a.anisoBorU), iop, false);
+ Tensor t = atomSetCollection.addRotatedTensor(a, symmetry
+ .getTensor(a.anisoBorU), iop, false);
t.isModulated = true;
if (Logger.debuggingHigh) {
- Logger.debug("setModulation Uij(final)=" + Escape.eAF(a.anisoBorU) +
"\n");
+ Logger.debug("setModulation Uij(final)=" + Escape.eAF(a.anisoBorU)
+ + "\n");
Logger.debug("setModulation tensor=" +
a.tensors.get(0).getInfo("all"));
}
}
@@ -345,10 +372,10 @@
sb.append(((int) t) + "\n");
}
// displace the atom and reverse the vector only if not filter "MODVIB"
-// if (!modVib) {
- // a.add(ms);
+ // if (!modVib) {
+ // a.add(ms);
// ms.setModT(true, Integer.MAX_VALUE);
- // }
+ // }
symmetry.toCartesian(ms, true);
//System.out.println("a.vib(xyz)=" + a.vib);
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-14 02:43:07 UTC (rev 18563)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/JanaReader.java
2013-08-14 10:38:00 UTC (rev 18564)
@@ -132,7 +132,7 @@
}
private void ndim() {
- setModDim(line.substring(line.length() - 1));
+ setModDim(parseIntStr(getTokens()[1]) - 3);
}
private int qicount;
@@ -253,17 +253,23 @@
P3 pt;
if (nOcc > 0 && !haveCrenel)
r.readLine(); //"1.00000"
+ int wv = 0;
+ float a1, a2;
for (int j = 0; j < nOcc; j++) {
if (haveCrenel) {
float[][] data = readM40FloatLines(2, 1, r);
- float w = data[0][0];
- float c = data[1][0];
- id = "O_0#0" + label;
- pt = P3.new3(c, w, 0);
- addModulation(null, id, pt, -1);
+ a1 = data[0][0];
+ a2 = data[1][0];
} else {
- addSinCos(j, "O_", label, r);
+ wv = j + 1;
+ readM40Floats(r);
+ a1 = floats[1];
+ a2 = floats[0];
}
+ id = "O_" + wv + "#0" + label;
+ pt = P3.new3(a1, a2, 0);
+ if (a1 != 0 || a2 != 0)
+ addModulation(null, id, pt, -1);
}
// read displacement data
Modified: trunk/Jmol/src/org/jmol/render/RepaintManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/RepaintManager.java 2013-08-14 02:43:07 UTC
(rev 18563)
+++ trunk/Jmol/src/org/jmol/render/RepaintManager.java 2013-08-14 10:38:00 UTC
(rev 18564)
@@ -106,10 +106,8 @@
if (repaintPending)
return false;
repaintPending = true;
- if (holdRepaint == 0) {
- //System.out.println("RM refresh() " + (test++));
+ if (holdRepaint == 0)
repaintNow(why);
- }
return true;
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-08-14 02:43:07 UTC
(rev 18563)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-08-14 10:38:00 UTC
(rev 18564)
@@ -308,7 +308,7 @@
}
if (haveError || !isJS || !allowJSThreads) {
viewer.setTainted(true);
- viewer.popHoldRepaint("executeCommands" + " " + scriptLevel);
+ viewer.popHoldRepaint("executeCommands" + " " + (scriptLevel > 0 ?
JC.REPAINT_IGNORE : ""));
}
timeEndExecution = System.currentTimeMillis();
if (errorMessage == null && executionStopped)
Modified: trunk/Jmol/src/org/jmol/util/Modulation.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-14 02:43:07 UTC
(rev 18563)
+++ trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-14 10:38:00 UTC
(rev 18564)
@@ -61,8 +61,9 @@
case TYPE_DISP_FOURIER:
case TYPE_OCC_FOURIER:
case TYPE_U_FOURIER:
- a1 = params.x;
- a2 = params.y;
+ a1 = params.x; // cos
+ a2 = params.y; // sin
+ //System.out.println("ccos=" + a1 + " csin=" + a2);
break;
case TYPE_DISP_SAWTOOTH:
case TYPE_OCC_CRENEL:
@@ -135,7 +136,7 @@
if (a2 != 0)
v += a2 * Math.sin(theta);
if (Logger.debuggingHigh)
- Logger.debug("MOD v " + v + " a1 a2 " + a1 + " " + a2 + " / " + theta
+ " " + ms.t);
+ Logger.debug("MOD v=" + v + " a1,a2=" + a1 + " " + a2 + " / theta=" +
theta + " id=" + ms.id);
break;
case TYPE_OCC_CRENEL:
@@ -147,6 +148,7 @@
x4 -= Math.floor(x4);
ms.v = (range(x4) ? 1 : 0);
+ ms.v0 = Float.NaN; // don't add this in
//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 2013-08-14 02:43:07 UTC
(rev 18563)
+++ trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-14 10:38:00 UTC
(rev 18564)
@@ -18,6 +18,7 @@
public float delta;
public P3 r;
public Matrix3f rot;
+ public float v0;
public float v = Float.NaN;
public int t;
public Map<String, Float> htValues;
Modified: trunk/Jmol/src/org/jmol/viewer/AnimationManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/AnimationManager.java 2013-08-14
02:43:07 UTC (rev 18563)
+++ trunk/Jmol/src/org/jmol/viewer/AnimationManager.java 2013-08-14
10:38:00 UTC (rev 18564)
@@ -53,23 +53,28 @@
public int lastFrameDelayMs;
public void setAnimationOn(boolean animationOn) {
+ if (animationOn == this.animationOn)
+ return;
+
if (!animationOn || !viewer.haveModelSet() || viewer.isHeadless()) {
stopThread(false);
return;
}
if (!viewer.getSpinOn())
- viewer.refresh(3, "Viewer:setAnimationOn");
+ viewer.refresh(3, "Anim:setAnimationOn");
setAnimationRange(-1, -1);
resumeAnimation();
}
public void stopThread(boolean isPaused) {
+ boolean stopped = false;
if (animationThread != null) {
animationThread.interrupt();
animationThread = null;
+ stopped = true;
}
animationPaused = isPaused;
- if (!viewer.getSpinOn())
+ if (stopped && !viewer.getSpinOn())
viewer.refresh(3, "Viewer:setAnimationOff");
animation(false);
stopModulationThread();
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