Revision: 18535
http://sourceforge.net/p/jmol/code/18535
Author: hansonr
Date: 2013-08-11 00:05:54 +0000 (Sun, 11 Aug 2013)
Log Message:
-----------
___JmolVersion="13.3.4_dev_2013.08.10"
new feature: MODULATION command -- for modulated structures
-- operates on currently selected set of atoms
-- MODULATION ON
-- MODULATION OFF
-- MODULATION t
-- sets modulation "t" of selected atoms
-- MODULATION PLAY t1 t2
-- animates a once-through sequence of t from t1 to t2
-- MODULATION FPS x.x // may be < 1
-- sets speed of animation
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
trunk/Jmol/src/org/jmol/api/JmolViewer.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/thread/MoveToThread.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
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/AtomSetChooser.java
Added Paths:
-----------
trunk/Jmol/src/org/jmol/thread/ModulationThread.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-10 14:03:58 UTC (rev 18534)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/ModulationReader.java
2013-08-11 00:05:54 UTC (rev 18535)
@@ -68,7 +68,6 @@
private P3 q1;
private V3 q1Norm;
- private Matrix3f rot;
private Map<String, P3> htModulation;
private Map<String, JmolList<Modulation>> htAtomMods;
private int modT;
@@ -77,7 +76,7 @@
protected void initializeMod() throws Exception {
modAxes = getFilter("MODAXES=");
- modVib = checkFilterKey("MODVIB");
+ modVib = checkFilterKey("MODVIB"); // then use MODULATION ON to see
modulation
modAverage = checkFilterKey("MODAVE");
checkSpecial = !checkFilterKey("NOSPECIAL");
atomSetCollection.setCheckSpecial(checkSpecial);
@@ -239,7 +238,6 @@
return;
atoms = atomSetCollection.getAtoms();
symmetry = atomSetCollection.getSymmetry();
- rot = new Matrix3f();
SB sb = new SB();
for (int i = atomSetCollection.getLastAtomSetAtomIndex(); i < n; i++)
modulateAtom(atoms[i], sb);
@@ -273,9 +271,10 @@
float epsilon = symmetry.getModParam(iop, 0);
float delta = symmetry.getModParam(iop, 1);
delta -= modT;
+ Matrix3f rot = new Matrix3f();
symmetry.getSpaceGroupOperation(iop).getRotationScale(rot);
- //System.out.println("=========MR i=" + a.index + " " + a.atomName + " " +
a + " " + a.occupancy);
- //System.out.println("op=" + (iop + 1) + " " +
symmetry.getSpaceGroupXyz(iop, false) + " ep=" + epsilon + " de=" + delta);
+ System.out.println("=========MR i=" + a.index + " " + a.atomName + " " + a
+ " " + a.occupancy);
+ System.out.println("op=" + (iop + 1) + " " +
symmetry.getSpaceGroupXyz(iop, false) + " ep=" + epsilon + " de=" + delta);
ModulationSet ms = new ModulationSet(list);
a.vib = ms;
ms.epsilon = epsilon;
@@ -312,7 +311,7 @@
// displace the atom and reverse the vector only if not filter "MODVIB"
if (!modVib) {
a.add(ms);
- ms.scale(-1);
+ ms.setModT(true, Integer.MAX_VALUE);
}
symmetry.toCartesian(ms, true);
//System.out.println("a.vib(xyz)=" + a.vib);
Modified: trunk/Jmol/src/org/jmol/api/JmolViewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolViewer.java 2013-08-10 14:03:58 UTC (rev
18534)
+++ trunk/Jmol/src/org/jmol/api/JmolViewer.java 2013-08-11 00:05:54 UTC (rev
18535)
@@ -617,6 +617,7 @@
* @return string from ScriptEvaluator#outputBuffer
*/
abstract public String runScript(String script);
+ abstract public int modelGetLastVibrationIndex(int i, int tok);
}
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-08-10
14:03:58 UTC (rev 18534)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-08-11
00:05:54 UTC (rev 18535)
@@ -2660,6 +2660,5 @@
}
-
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-08-10
14:03:58 UTC (rev 18534)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-08-11
00:05:54 UTC (rev 18535)
@@ -53,6 +53,7 @@
import org.jmol.util.BS;
import org.jmol.util.BoxInfo;
import org.jmol.util.Elements;
+import org.jmol.util.ModulationSet;
import org.jmol.util.P3;
import org.jmol.util.P4;
import org.jmol.util.Tensor;
@@ -1499,13 +1500,15 @@
return unitCells[modelIndex].getCellRange();
}
- public boolean modelHasVibrationVectors(int modelIndex) {
+ public int getLastVibrationVector(int modelIndex, int tok) {
if (vibrations != null)
for (int i = atomCount; --i >= 0;)
if ((modelIndex < 0 || atoms[i].modelIndex == modelIndex)
- && vibrations[i] != null && vibrations[i].length() > 0)
- return true;
- return false;
+ && vibrations[i] != null
+ && vibrations[i].length() > 0
+ && (tok == 0 || (tok == T.modulation) == (vibrations[i] instanceof
ModulationSet)))
+ return i;
+ return -1;
}
public BS getElementsPresentBitSet(int modelIndex) {
@@ -2705,8 +2708,7 @@
sb.append(" name=").append(Escape.eS(getModelName(i)))
.append(" title=").append(Escape.eS(
getModelTitle(i)))
- .append(" hasVibrationVectors=\"").appendB(
- modelHasVibrationVectors(i)).append("\" />");
+ .append("
hasVibrationVectors=\"").appendB(viewer.modelHasVibrationVectors(i)).append("\"
/>");
}
sb.append("\n</models>");
return sb.toString();
@@ -3438,4 +3440,42 @@
return ilist;
}
+ public void setModulation(BS bs, boolean isOn, int t) {
+ //System.out.println("setModulation " + isOn + " " + t);
+ for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+ Vibration v = getVibration(i, false);
+ if (!(v instanceof ModulationSet))
+ continue;
+ ModulationSet ms = (ModulationSet) v;
+ Atom a = atoms[i];
+ boolean wasEnabled = ms.enabled;
+ //System.out.println(a.x + " " + a.y + " " + a.z + " ms was " + ms + " "
+ wasEnabled + " " + ms.t);
+ switch (ms.setModT(isOn, t)) {
+ case 0:
+ continue;
+ case 1: // now off
+ case 2: // now on
+ a.sub(ms);
+ break;
+ case 3: // new t
+ // will turn on modulation
+ // must convert to Cartesians
+ getUnitCell(a.modelIndex).toCartesian(ms, true);
+ //System.out.println("ms now1 " + ms + " " + ms.enabled + " " + ms.t);
+ if (wasEnabled)
+ a.add(ms.prevSetting);
+ ms.setModT(true, Integer.MAX_VALUE);
+ a.sub(ms);
+ //System.out.println(a.x + " " + a.y + " " + a.z + " ms now " + ms + "
" + ms.enabled + " " + ms.t);
+ break;
+ case 4: // unchanged t
+ ms.setModT(true, Integer.MAX_VALUE);
+ if (!wasEnabled)
+ a.sub(ms);
+ break;
+ }
+ //System.out.println(a.x + " " + a.y + " " + a.z + " ms is " + ms + " "
+ ms.enabled + " " + ms.t);
+ }
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-08-10 14:03:58 UTC
(rev 18534)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-08-11 00:05:54 UTC
(rev 18535)
@@ -5773,6 +5773,9 @@
case T.minimize:
minimize();
break;
+ case T.modulation:
+ modulation();
+ break;
case T.move:
move();
break;
@@ -12524,6 +12527,31 @@
setShapeSizeBs(shapeType, mad, null);
}
+ private void modulation() throws ScriptException {
+ boolean mod = false;
+ switch (getToken(1).tok) {
+ case T.on:
+ mod = true;
+ //$FALL-THROUGH$
+ case T.off:
+ if (!chk)
+ viewer.setModulation(mod, Integer.MAX_VALUE, Integer.MAX_VALUE, false);
+ break;
+ case T.integer:
+ if (!chk)
+ viewer.setModulation(true, intParameter(1), Integer.MAX_VALUE, false);
+ break;
+ case T.fps:
+ if (!chk)
+ viewer.setModulationFps(floatParameter(2));
+ break;
+ case T.play:
+ if (!chk)
+ viewer.setModulation(true, intParameter(2), intParameter(3), false);
+ break;
+ }
+ }
+
private void animation() throws ScriptException {
boolean animate = false;
switch (getToken(1).tok) {
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2013-08-10 14:03:58 UTC (rev
18534)
+++ trunk/Jmol/src/org/jmol/script/T.java 2013-08-11 00:05:54 UTC (rev
18535)
@@ -700,6 +700,7 @@
final static int write = 21 | 0 << 9 | mathfunc | scriptCommand;
final static int cache = 22 | 0 << 9 | mathfunc | scriptCommand;
// new in Jmol 13.1.2
final static int tensor = 23 | 0 << 9 | mathfunc | mathproperty;
+ public final static int modulation = 24 | 0 << 9 | mathfunc |
scriptCommand;
// xxx(a)
@@ -1645,6 +1646,7 @@
"mo", T.t(mo),
"model", T.t(model),
"models", null,
+ "modulation", T.t(modulation),
"move", T.t(move),
"moveTo", T.t(moveto),
"navigate", T.t(navigate),
Added: trunk/Jmol/src/org/jmol/thread/ModulationThread.java
===================================================================
--- trunk/Jmol/src/org/jmol/thread/ModulationThread.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/thread/ModulationThread.java 2013-08-11
00:05:54 UTC (rev 18535)
@@ -0,0 +1,115 @@
+/* $RCSfile$
+ * $Author$
+ * $Date$
+ * $Revision$
+ *
+ * Copyright (C) 2011 The Jmol Development Team
+ *
+ * Contact: jmol-develop...@lists.sf.net
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
+ * 02110-1301, USA.
+ */
+
+package org.jmol.thread;
+
+import org.jmol.util.Logger;
+import org.jmol.viewer.AnimationManager;
+import org.jmol.viewer.Viewer;
+
+public class ModulationThread extends JmolThread {
+ /**
+ *
+ */
+ private int modT;
+ private final int modT2;
+
+ private AnimationManager animationManager;
+
+
+ public ModulationThread(AnimationManager animationManager, Viewer viewer,
int modT1, int modT2) {
+ super();
+ setViewer(viewer, "ModulationThread");
+ modT = modT1;
+ this.modT2 = modT2;
+ this.animationManager = animationManager;
+ viewer.startHoverWatcher(false);
+ }
+
+ @Override
+ public void interrupt() {
+ if (stopped)
+ return;
+ stopped = true;
+ if (Logger.debugging)
+ Logger.debug("animation thread interrupted!");
+ animationManager.modulationPlay = false;
+ try {
+ } catch (Exception e) {
+ // null pointer -- don't care;
+ }
+ super.interrupt();
+ }
+
+ @Override
+ protected void run1(int mode) throws InterruptedException {
+ while (true) {
+ //System.out.println("AnimationThread " + mode + " " + this + " " +
sleepTime);
+ switch (mode) {
+ case INIT:
+ if (Logger.debugging)
+ Logger.debug("modulation thread running");
+ viewer.requestRepaintAndWait();
+ viewer.startHoverWatcher(false);
+ mode = MAIN;
+ break;
+ case MAIN:
+ //System.out.println("anim thred " +
animationManager.getCurrentFrame() +" "+ framePointer);
+ if (checkInterrupted() || !animationManager.modulationPlay || modT >
modT2) {
+ mode = FINISH;
+ break;
+ }
+ mode = CHECK1;
+ break;
+ case CHECK1:
+ viewer.setModulation(true, modT++, Integer.MAX_VALUE, true);
+ mode = CHECK2;
+ break;
+ case CHECK2:
+ targetTime += (int) (1000f / animationManager.modulationFps);
+ mode = CHECK3;
+ break;
+ case CHECK3:
+ while (animationManager.modulationPlay && !checkInterrupted()
+ && !viewer.getRefreshing()) {
+ if (!runSleep(10, CHECK3))
+ return;
+ }
+ viewer.refresh(1, "modulationThread");
+ sleepTime = (int) (targetTime - (System.currentTimeMillis() -
startTime));
+ if (!runSleep(sleepTime, MAIN))
+ return;
+ mode = MAIN;
+ break;
+ case FINISH:
+ if (Logger.debugging)
+ Logger.debug("modulation thread exiting");
+ animationManager.stopModulationThread();
+ return;
+ }
+ }
+ }
+
+}
\ No newline at end of file
Modified: trunk/Jmol/src/org/jmol/thread/MoveToThread.java
===================================================================
--- trunk/Jmol/src/org/jmol/thread/MoveToThread.java 2013-08-10 14:03:58 UTC
(rev 18534)
+++ trunk/Jmol/src/org/jmol/thread/MoveToThread.java 2013-08-11 00:05:54 UTC
(rev 18535)
@@ -226,10 +226,14 @@
}
private void setValues(float fStep) {
+ if (cameraDepth != null)
+ transformManager.setCameraDepthPercent(cameraDepth.getVal(fStep), false);
+ if (cameraX != null && cameraY != null)
+ transformManager.setCamera(cameraX.getVal(fStep), cameraY.getVal(fStep));
+ if (zoom != null)
+ transformManager.zoomToPercent(zoom.getVal(fStep));
transformManager.modelRadius = rotationRadius.getVal(fStep);
transformManager.scaleDefaultPixelsPerAngstrom = pixelScale.getVal(fStep);
- if (zoom != null)
- transformManager.zoomToPercent(zoom.getVal(fStep));
if (xTrans != null && yTrans != null) {
transformManager.translateToPercent('x', xTrans.getVal(fStep));
transformManager.translateToPercent('y', yTrans.getVal(fStep));
@@ -239,10 +243,6 @@
.getVal(fStep));
if (navDepth != null)
transformManager.setNavigationDepthPercent(navDepth.getVal(fStep));
- if (cameraDepth != null)
- transformManager.setCameraDepthPercent(cameraDepth.getVal(fStep), false);
- if (cameraX != null && cameraY != null)
- transformManager.setCamera(cameraX.getVal(fStep), cameraY.getVal(fStep));
}
@Override
Modified: trunk/Jmol/src/org/jmol/util/Modulation.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-10 14:03:58 UTC
(rev 18534)
+++ trunk/Jmol/src/org/jmol/util/Modulation.java 2013-08-11 00:05:54 UTC
(rev 18535)
@@ -19,6 +19,8 @@
private double left, right;
private V3 nq; // wave vector
+ private double nqlen;
+
private int fn; // power
private char axis;
private final int type;
@@ -50,6 +52,7 @@
*/
public Modulation(P3 nq, char axis, int type, int fn, P3 params, String
utens) {
this.nq = V3.newV(nq);
+ nqlen = nq.length();
this.axis = axis;
this.type = type;
this.fn = fn;
@@ -120,7 +123,7 @@
//if (type == TYPE_OCC_CRENEL)
//delta = 0;
- double x4 = ms.epsilon * (nq.dot(ms.r) - fn * ms.delta + fn * ms.t);
+ double x4 = ms.epsilon * (nq.dot(ms.r) - fn * ms.delta + nqlen * ms.t);
switch (type) {
case TYPE_DISP_FOURIER:
@@ -131,6 +134,7 @@
v += a1 * Math.cos(theta);
if (a2 != 0)
v += a2 * Math.sin(theta);
+ //System.out.println("MOD v " + v + " a1 a2 " + a1 + " " + a2 + " / " +
theta + " " + ms.t);
break;
case TYPE_OCC_CRENEL:
Modified: trunk/Jmol/src/org/jmol/util/ModulationSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-10 14:03:58 UTC
(rev 18534)
+++ trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-11 00:05:54 UTC
(rev 18535)
@@ -21,6 +21,7 @@
public float v = Float.NaN;
public int t;
public Map<String, Float> htValues;
+ public boolean enabled = false;
public ModulationSet(JmolList<Modulation> list) {
mods = list;
@@ -46,4 +47,33 @@
htValues.put(utens, Float.valueOf(f == null ? v : f.floatValue() + v));
}
+ public V3 prevSetting;
+
+ /**
+ * Set modulation "t" value, which sets which unit cell in sequence we are
looking at.
+ *
+ * @param isOn
+ * @param t
+ * @return 0 (no change), 1 (disabled), 2 (enabled), 3 (new t), 4 (same t)
+ *
+ */
+ public int setModT(boolean isOn, int t) {
+ if (t == Integer.MAX_VALUE) {
+ if (enabled == isOn)
+ return 0;
+ enabled = isOn;
+ scale(-1);
+ return (enabled ? 2 : 1);
+ }
+ if (t == this.t)
+ return 4;
+ if (prevSetting == null)
+ prevSetting = new V3();
+ prevSetting.setT(this);
+ this.t = t;
+ calculate();
+ enabled = false;
+ return 3;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/AnimationManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/AnimationManager.java 2013-08-10
14:03:58 UTC (rev 18534)
+++ trunk/Jmol/src/org/jmol/viewer/AnimationManager.java 2013-08-11
00:05:54 UTC (rev 18535)
@@ -27,6 +27,7 @@
import java.util.Map;
import org.jmol.thread.AnimationThread;
+import org.jmol.thread.ModulationThread;
import org.jmol.util.BS;
import org.jmol.util.BSUtil;
//import org.jmol.util.JmolList;
@@ -37,6 +38,7 @@
public class AnimationManager {
private AnimationThread animationThread;
+ private ModulationThread modulationThread;
private Viewer viewer;
AnimationManager(Viewer viewer) {
@@ -70,7 +72,9 @@
if (!viewer.getSpinOn())
viewer.refresh(3, "Viewer:setAnimationOff");
animation(false);
+ stopModulationThread();
viewer.setStatusFrameChanged(false);
+
}
public boolean setAnimationNext() {
@@ -300,6 +304,18 @@
lastFramePainted = currentAnimationFrame;
}
+ public void setModulationPlay(int modT1, int modT2) {
+ if (modT1 == Integer.MAX_VALUE || !viewer.haveModelSet() ||
viewer.isHeadless()) {
+ stopThread(false);
+ return;
+ }
+ if (modulationThread == null) {
+ modulationPlay = true;
+ modulationThread = new ModulationThread(this, viewer, modT1, modT2);
+ modulationThread.start();
+ }
+ }
+
void resumeAnimation() {
if(currentModelIndex < 0)
setAnimationRange(firstFrameIndex, lastFrameIndex);
@@ -411,7 +427,17 @@
private int lastFramePainted;
private int lastModelPainted;
private int intAnimThread;
+ public boolean modulationPlay;
+ public float modulationFps = 1;
+ public BS bsModulating;
+ public void setModulationFps(float fps) {
+ if (fps > 0)
+ modulationFps = fps;
+ else
+ stopModulationThread();
+ }
+
private void setViewer(boolean clearBackgroundModel) {
viewer.setTrajectory(currentModelIndex);
viewer.setFrameOffset(currentModelIndex);
@@ -511,5 +537,13 @@
return frameStep * direction * currentDirection;
}
+ public void stopModulationThread() {
+ if (modulationThread != null) {
+ modulationThread.interrupt();
+ modulationThread = null;
+ }
+ modulationPlay = false;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-10 14:03:58 UTC
(rev 18534)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-11 00:05:54 UTC
(rev 18535)
@@ -11,8 +11,21 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.3.4_dev_2013.08.09"
+___JmolVersion="13.3.4_dev_2013.08.10"
+new feature: MODULATION command -- for modulated structures
+ -- operates on currently selected set of atoms
+ -- MODULATION ON
+ -- MODULATION OFF
+ -- MODULATION t
+ -- sets modulation "t" of selected atoms
+ -- MODULATION PLAY t1 t2
+ -- animates a once-through sequence of t from t1 to t2
+ -- MODULATION FPS x.x // may be < 1
+ -- sets speed of animation
+
+bug fix: zoom setting lost in state
+
code: incommensurate crystal work -- Uiso, preliminary Uij and subsystems
code: incommensurate crystal work -- occupancy Crenel, displacive sawtooths
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2013-08-10 14:03:58 UTC
(rev 18534)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2013-08-11 00:05:54 UTC
(rev 18535)
@@ -642,8 +642,7 @@
s = (String) m.getModelAuxiliaryInfoValue(i, "modelID");
if (s != null)
model.put("id", s);
- model.put("vibrationVectors", Boolean.valueOf(m
- .modelHasVibrationVectors(i)));
+ model.put("vibrationVectors",
Boolean.valueOf(viewer.modelHasVibrationVectors(i)));
Model mi = m.models[i];
model.put("atomCount", Integer.valueOf(mi.atomCount));
model.put("bondCount", Integer.valueOf(mi.getBondCount()));
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-08-10 14:03:58 UTC
(rev 18534)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-08-11 00:05:54 UTC
(rev 18535)
@@ -79,6 +79,7 @@
import org.jmol.util.JmolEdge;
import org.jmol.util.JmolFont;
import org.jmol.util.Logger;
+import org.jmol.util.ModulationSet;
import org.jmol.util.Parser;
import org.jmol.util.P3;
import org.jmol.util.SB;
@@ -290,8 +291,7 @@
if (bs.isEmpty())
ms.haveHiddenBonds = false;
else
- commands.append(" hide ").append(Escape.eBond(bs)).append(
- ";\n");
+ commands.append(" hide ").append(Escape.eBond(bs)).append(";\n");
}
// shape construction
@@ -317,12 +317,12 @@
String s = (String) ms.getModelAuxiliaryInfoValue(i, "modelID");
if (s != null
&& !s.equals(ms.getModelAuxiliaryInfoValue(i, "modelID0")))
- commands.append(fcmd).append("; frame ID ").append(
- Escape.eS(s)).append(";\n");
+ commands.append(fcmd).append("; frame ID ").append(Escape.eS(s))
+ .append(";\n");
String t = ms.frameTitles[i];
if (t != null && t.length() > 0)
- commands.append(fcmd).append("; frame title ").append(
- Escape.eS(t)).append(";\n");
+ commands.append(fcmd).append("; frame title ").append(Escape.eS(t))
+ .append(";\n");
if (needOrientations && models[i].orientation != null
&& !ms.isTrajectorySubFrame(i))
commands.append(fcmd).append("; ").append(
@@ -339,6 +339,7 @@
}
if (ms.unitCells != null) {
+ boolean haveModulation = false;
for (int i = 0; i < modelCount; i++) {
SymmetryInterface symmetry = ms.getUnitCell(i);
if (symmetry == null)
@@ -351,12 +352,30 @@
if (pt != null)
commands.append("; set unitcell ").append(Escape.eP(pt));
commands.append(";\n");
+ haveModulation |= (viewer.modelGetLastVibrationIndex(i,
T.modulation) >= 0);
}
getShapeState(commands, isAll, JC.SHAPE_UCCAGE);
// if (viewer.getObjectMad(StateManager.OBJ_UNITCELL) == 0)
// commands.append(" unitcell OFF;\n");
+ if (haveModulation) {
+ //commands.append(" modulation fps "
+ // + viewer.animationManager.modulationFps + ";\n");
+ Map<String, BS> temp = new Hashtable<String, BS>();
+ int ivib;
+ for (int i = modelCount; --i >= 0;) {
+ if ((ivib = viewer.modelGetLastVibrationIndex(i, T.modulation)) >=
0)
+ for (int j = models[i].firstAtomIndex; j <= ivib; j++) {
+ ModulationSet mset = (ModulationSet) viewer.getVibration(j);
+ if (mset.enabled)
+ BSUtil.setMapBitSet(temp, j, j, "modulation " + mset.t);
+ }
+ }
+ String s = getCommands(temp, null, "select");
+ commands.append(s);
+ }
}
- commands.append(" set fontScaling " + viewer.getBoolean(T.fontscaling)
+ ";\n");
+ commands.append(" set fontScaling " + viewer.getBoolean(T.fontscaling)
+ + ";\n");
if (viewer.getBoolean(T.modelkitmode))
commands.append(" set modelKitMode true;\n");
}
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2013-08-10
14:03:58 UTC (rev 18534)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2013-08-11
00:05:54 UTC (rev 18535)
@@ -2064,8 +2064,7 @@
return;
period = -period;
}
- setVibrationOn(period > 0
- && viewer.modelHasVibrationVectors(viewer.getCurrentModelIndex()));
+ setVibrationOn(period > 0 &&
viewer.modelGetLastVibrationIndex(viewer.getCurrentModelIndex(), 0) >= 0);
}
public void setVibrationT(float t) {
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-10 14:03:58 UTC (rev
18534)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-11 00:05:54 UTC (rev
18535)
@@ -3130,8 +3130,13 @@
}
@Override
+ public int modelGetLastVibrationIndex(int modelIndex, int tok) {
+ return modelSet.getLastVibrationVector(modelIndex, tok);
+ }
+
+ @Override
public boolean modelHasVibrationVectors(int modelIndex) {
- return modelSet.modelHasVibrationVectors(modelIndex);
+ return (modelSet.getLastVibrationVector(modelIndex, T.vibration) >= 0);
}
@Override
@@ -10174,4 +10179,20 @@
return (!getTestFlag(1));
}
+ public void setModulation(boolean isOn, int t1, int t2, boolean isThread) {
+ if (t2 == Integer.MAX_VALUE) {
+ if (!isThread)
+ animationManager.setModulationPlay(Integer.MAX_VALUE, 0);
+ if (t1 != Integer.MAX_VALUE)
+ global.setI("_modt", t1);
+ modelSet.setModulation(getSelectionSet(false), isOn, t1);
+ } else {
+ animationManager.setModulationPlay(t1, t2);
+ }
+ }
+
+ public void setModulationFps(float fps) {
+ animationManager.setModulationFps(fps);
+ }
+
}
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/AtomSetChooser.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/AtomSetChooser.java
2013-08-10 14:03:58 UTC (rev 18534)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/AtomSetChooser.java
2013-08-11 00:05:54 UTC (rev 18535)
@@ -588,7 +588,7 @@
// search till get to either end of found a frequency
while (index >= 0 && index < maxIndex
- && !(foundFrequency=viewer.modelHasVibrationVectors(indexes[index]))) {
+ &&
!(foundFrequency=(viewer.modelHasVibrationVectors(indexes[index])))) {
index+=increment;
}
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