Revision: 21017
http://sourceforge.net/p/jmol/code/21017
Author: hansonr
Date: 2016-03-23 04:35:05 +0000 (Wed, 23 Mar 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.4_2016.03.23"
new feature: load =magndata/1.1.37
-- links to the MAGNDATA database at http://webbdcrista1.ehu.es/magndata
-- "magndata", "http://webbdcrista1.ehu.es/magndata/mcif/%FILE.mcif";,
new feature: set vectorTrail n
-- adds a trail onto a modulating vector (as for an incommensurate magnetic
spin)
-- n trails are made, typically in a fan-like pattern that trails the spinning
vector
load =magndata/1.1.37
set vectortrace 20
set vibrationperiod 2
vibration on
new feature: unitcell ON adds #nnn (international table number) to cell
description if found
bug fix: {*}.find("CHEMICAL","NAMES") only reports one name.
code: more efficient identifying space group
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
branches/v14_4/Jmol/src/org/jmol/script/T.java
branches/v14_4/Jmol/src/org/jmol/util/Vibration.java
branches/v14_4/Jmol/src/org/jmol/viewer/GlobalSettings.java
branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/util/Vibration.java
trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: branches/v14_4/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java
2016-03-22 18:50:47 UTC (rev 21016)
+++ branches/v14_4/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java
2016-03-23 04:35:05 UTC (rev 21017)
@@ -37,6 +37,7 @@
import javajs.util.P3;
import javajs.util.P3i;
+import javajs.util.T3;
import javajs.util.V3;
import org.jmol.util.Vibration;
@@ -67,6 +68,10 @@
private boolean vibrationOn;
private boolean drawCap;
private boolean showModVecs;
+ private int vectorTrace;
+ private P3 ptTemp4;
+ private P3 ptTemp3;
+ private P3 ptTemp2;
@Override
@@ -81,6 +86,7 @@
short[] colixes = vectors.colixes;
boolean needTranslucent = false;
vectorScale = vwr.getFloat(T.vectorscale);
+ vectorTrace = vwr.getInt(T.vectortrail);
if (vectorScale < 0)
vectorScale = 1;
vectorSymmetry = vwr.getBoolean(T.vectorsymmetry);
@@ -115,14 +121,14 @@
needTranslucent = true;
continue;
}
- renderVector(atom);
+ renderVector(atom, vib);
if (vectorSymmetry) {
if (vibTemp == null)
vibTemp = new Vibration();
vibTemp.setT(vib);
vibTemp.scale(-1);
transform(mads[i], atom, vibTemp, null);
- renderVector(atom);
+ renderVector(atom, vib);
}
}
if (haveModulations)
@@ -133,21 +139,22 @@
JmolModulationSet mod = ms.getModulation(i);
if (mod == null)
continue;
+ if (!g3d.setC(Shape.getColix(colixes, i, atom))) {
+ needTranslucent = true;
+ continue;
+ }
// now we focus on modulations
// this may involve a modulated atom or a spin modulation
if (!transform(mads[i], atom, null, mod))
continue;
- if (!g3d.setC(Shape.getColix(colixes, i, atom))) {
- needTranslucent = true;
- continue;
- }
- renderVector(atom);
+ renderVector(atom, null);
}
return needTranslucent;
}
- private boolean transform(short mad, Atom atom, Vibration vib,
JmolModulationSet mod2) {
+ private boolean transform(short mad, Atom atom, Vibration vib,
+ JmolModulationSet mod2) {
boolean isMod = (vib == null || vib.modDim >= 0);
boolean isSpin = (!isMod && vib.modDim == Vibration.TYPE_SPIN);
if (vib == null)
@@ -188,15 +195,15 @@
headOffsetVector.scale(headScale / headOffsetVector.length());
} else if (vectorsCentered || isSpin) {
standardVector = false;
- // Vibration v;
- // if (mod2 == null || !mod2.isEnabled()) {
- // v = vib;
-// } else {
-// v = vibTemp;
-// vibTemp.set(0, 0, 0);
-// v.setTempPoint(vibTemp, null, 1, vwr.g.modulationScale);
-// vwr.tm.getVibrationPoint(vib, v, Float.NaN);
-// }
+ // Vibration v;
+ // if (mod2 == null || !mod2.isEnabled()) {
+ // v = vib;
+ // } else {
+ // v = vibTemp;
+ // vibTemp.set(0, 0, 0);
+ // v.setTempPoint(vibTemp, null, 1, vwr.g.modulationScale);
+ // vwr.tm.getVibrationPoint(vib, v, Float.NaN);
+ // }
pointVectorEnd.scaleAdd2(0.5f * vectorScale, vib, ptTemp);
pointVectorStart.scaleAdd2(-0.5f * vectorScale, vib, ptTemp);
} else {
@@ -212,6 +219,7 @@
tm.transformPtScrT3(pointArrowHead, screenArrowHead);
}
}
+
if (!standardVector) {
tm.transformPtScrT3(pointVectorEnd, screenVectorEnd);
tm.transformPtScrT3(pointVectorStart, screenVectorStart);
@@ -226,10 +234,30 @@
headWidthPixels = diameter << 1;
if (headWidthPixels < diameter + 2)
headWidthPixels = diameter + 2;
+
return true;
}
- private void renderVector(Atom atom) {
+ private void renderVector(Atom atom, Vibration vib) {
+ if (vib != null && vectorTrace > 0) {// show trace
+ if (ptTemp4 == null) {
+ ptTemp3 = new P3();
+ ptTemp4 = new P3();
+ ptTemp2 = new P3();
+ }
+ int d = Math.max(1, diameter >> 2);
+ P3[] pts = vib.addTracePt(vectorTrace, pointVectorEnd);
+ tm.transformPtScrT3(atom, ptTemp4);
+ if (pts != null)
+ for (int i = pts.length, p = vectorTrace; --i >= 0;) {
+ P3 pt = pts[--p];
+ if (pt == null)
+ break;
+ tm.transformPtScrT3(pt, ptTemp2);
+ g3d.fillCylinderBits(GData.ENDCAPS_FLAT, d, ptTemp4, ptTemp2);
+ }
+ }
+
if (drawShaft) {
pTemp3.set(atom.sX, atom.sY, atom.sZ);
if (standardVector)
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2016-03-22
18:50:47 UTC (rev 21016)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2016-03-23
04:35:05 UTC (rev 21017)
@@ -4590,7 +4590,7 @@
} else if (!isData) {
if (localName != null)
localName = vwr.fm.getFilePath(localName, false, false);
- if (!filename.equals("string") && !filename.equals("String[]"))
+ if (!filename.equals("String[]"))
loadScript.append("/*file*/").append(
(localName != null ? PT.esc(localName) : "$FILENAME$"));
}
@@ -7885,6 +7885,9 @@
break;
case 3:
switch (tokAt(1)) {
+ case T.trace:
+ setIntProperty("vectorTrace", intParameterRange(2, 0, 20));
+ return;
case T.scale:
if (!Float.isNaN(value = floatParameterRange(2, -100, 100)))
setFloatProperty("vectorScale", value);
Modified: branches/v14_4/Jmol/src/org/jmol/script/T.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/T.java 2016-03-22 18:50:47 UTC
(rev 21016)
+++ branches/v14_4/Jmol/src/org/jmol/script/T.java 2016-03-23 04:35:05 UTC
(rev 21017)
@@ -934,6 +934,7 @@
public final static int strandcountformeshribbon = intparam | 52;
public final static int strandcountforstrands = intparam | 54;
public final static int strutspacing = intparam | 56;
+ public final static int vectortrail = intparam | 57;
public final static int zdepth = intparam | 58;
public final static int zslab = intparam | 60;
public final static int zshadepower = intparam | 62;
@@ -1081,9 +1082,9 @@
public final static int usenumberlocalization = booleanparam | 195;
public final static int vectorscentered = booleanparam | 196;
public final static int vectorsymmetry = booleanparam | 197;
- public final static int waitformoveto = booleanparam | 198;
- public final static int windowcentered = booleanparam | 199;
- public final static int wireframerotation = booleanparam | 200;
+ public final static int waitformoveto = booleanparam | 199;
+ public final static int windowcentered = booleanparam | 200;
+ public final static int wireframerotation = booleanparam | 201;
public final static int zerobasedxyzrasmol = booleanparam | 202;
public final static int zoomenabled = booleanparam | 204;
public final static int zoomheight = booleanparam | 206;
@@ -2435,6 +2436,7 @@
"vectorScale",
"vectorsCentered",
"vectorSymmetry",
+ "vectorTrail",
"vibrationPeriod",
"vibrationScale",
"visualRange",
@@ -3472,6 +3474,7 @@
vectorscale, // "vectorScale"
vectorscentered, // "vectorsCenered"
vectorsymmetry, // "vectorSymmetry"
+ vectortrail, // "vectorTrail"
vibrationperiod, // "vibrationPeriod"
vibrationscale, // "vibrationScale"
visualrange, // "visualRange"
Modified: branches/v14_4/Jmol/src/org/jmol/util/Vibration.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/util/Vibration.java 2016-03-22
18:50:47 UTC (rev 21016)
+++ branches/v14_4/Jmol/src/org/jmol/util/Vibration.java 2016-03-23
04:35:05 UTC (rev 21017)
@@ -2,6 +2,7 @@
import java.util.Map;
+import javajs.util.P3;
import javajs.util.T3;
import javajs.util.V3;
@@ -88,4 +89,32 @@
return Integer.MIN_VALUE;
}
+ public boolean showTrace;
+ private P3[] trace = null;
+ public int tracePt;
+
+ public void startTrace(int n) {
+ trace = new P3[n];
+ tracePt = n;
+ }
+
+ public P3[] addTracePt(int n, Point3fi ptNew) {
+ if (ptNew == null || trace == null || n == 0 || n > trace.length)
+ startTrace(n);
+ if (ptNew != null && n > 2) {
+ if (--tracePt <= 0) {
+ P3 p0 = trace[trace.length - 1];
+ for (int i = trace.length; --i >= 1;)
+ trace[i] = trace[i-1];
+ trace[1] = p0;
+ tracePt = 1;
+ }
+ P3 p = trace[tracePt];
+ if (p == null)
+ p = trace[tracePt] = new P3();
+ p.setT(ptNew);
+ }
+ return trace;
+ }
+
}
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/GlobalSettings.java 2016-03-22
18:50:47 UTC (rev 21016)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/GlobalSettings.java 2016-03-23
04:35:05 UTC (rev 21017)
@@ -379,6 +379,7 @@
setB("vectorsCentered", vectorsCentered);
setF("vectorScale", vectorScale);
setB("vectorSymmetry", vectorSymmetry);
+ setI("vectorTrail", vectorTrail);
setF("vibrationPeriod", vibrationPeriod);
setF("vibrationScale", vibrationScale);
setB("waitForMoveTo", waitForMoveTo);
@@ -629,6 +630,7 @@
float vectorScale = 1f;
boolean vectorSymmetry = false; // Jmol 12.3.2
boolean vectorsCentered = false; // Jmol 14.1.14
+ int vectorTrail = 0; // Jmol 14.4.4
float vibrationPeriod = 1f;
float vibrationScale = 1f;
boolean wireframeRotation = false;
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2016-03-22 18:50:47 UTC
(rev 21016)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2016-03-23 04:35:05 UTC
(rev 21017)
@@ -68,6 +68,7 @@
"map",
"http://www.ebi.ac.uk/pdbe/api/%TYPE/%FILE?pretty=false&metadata=true";,
"rna3d", "http://rna.bgsu.edu/rna3dhub/%TYPE/download/%FILE";,
"aflow",
"http://aflowlib.mems.duke.edu/users/jmolers/binary_new/%FILE.aflow_binary";,
+ "magndata", "http://webbdcrista1.ehu.es/magndata/mcif/%FILE.mcif";,
// _#CHANGEABLE_ flag indicates that the loaded file should be saved in
any state in full
// ' at start indicates a Jmol script evaluation
"ams", "'http://rruff.geo.arizona.edu/AMS/viewJmol.php?'+(0+'%file'==0?
'mineral':('%file'.length==7? 'amcsd':'id'))+'=%file&action=showcif#_DOCACHE_'",
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-22
18:50:47 UTC (rev 21016)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-23
04:35:05 UTC (rev 21017)
@@ -10,8 +10,21 @@
Jmol.___JmolVersion="14.4.4_2016.03.23"
+new feature: load =magndata/1.1.37
+ -- links to the MAGNDATA database at http://webbdcrista1.ehu.es/magndata
+ -- "magndata", "http://webbdcrista1.ehu.es/magndata/mcif/%FILE.mcif";,
+
+new feature: set vectorTrail n
+ -- adds a trail onto a modulating vector (as for an incommensurate magnetic
spin)
+ -- n trails are made, typically in a fan-like pattern that trails the
spinning vector
+ load =magndata/1.1.37
+ set vectortrace 20
+ set vibrationperiod 2
+ vibration on
+
new feature: unitcell ON adds #nnn (international table number) to cell
description if found
+
bug fix: {*}.find("CHEMICAL","NAMES") only reports one name.
code: more efficient identifying space group
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2016-03-22 18:50:47 UTC
(rev 21016)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2016-03-23 04:35:05 UTC
(rev 21017)
@@ -1884,7 +1884,7 @@
htParams.put(
"loadScript",
loadScript = new SB().append(PT.rep(loadScript.toString(),
- "$FILENAME$", "data \"model inline\"\n" + strModel
+ "/*file*/$FILENAME$", "/*data*/data \"model inline\"\n" +
strModel
+ "end \"model inline\"")));
}
if (strModel != null) {
@@ -5038,6 +5038,8 @@
return g.smallMoleculeMaxAtoms;
case T.strutspacing:
return g.strutSpacing;
+ case T.vectortrail:
+ return g.vectorTrail;
}
Logger.error("viewer.getInt(" + T.nameOf(tok) + ") - not listed");
return 0;
@@ -5774,6 +5776,9 @@
case T.scriptreportinglevel:
value = eval.setStatic(tok, value);
break;
+ case T.vectortrail:
+ g.vectorTrail = value;
+ break;
case T.bondingversion:
// 14.1.11
value = (value == 0 ? Elements.RAD_COV_IONIC_OB1_100_1
Modified: trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java 2016-03-22
18:50:47 UTC (rev 21016)
+++ trunk/Jmol/src/org/jmol/renderspecial/VectorsRenderer.java 2016-03-23
04:35:05 UTC (rev 21017)
@@ -37,6 +37,7 @@
import javajs.util.P3;
import javajs.util.P3i;
+import javajs.util.T3;
import javajs.util.V3;
import org.jmol.util.Vibration;
@@ -67,6 +68,10 @@
private boolean vibrationOn;
private boolean drawCap;
private boolean showModVecs;
+ private int vectorTrace;
+ private P3 ptTemp4;
+ private P3 ptTemp3;
+ private P3 ptTemp2;
@Override
@@ -81,6 +86,7 @@
short[] colixes = vectors.colixes;
boolean needTranslucent = false;
vectorScale = vwr.getFloat(T.vectorscale);
+ vectorTrace = vwr.getInt(T.vectortrail);
if (vectorScale < 0)
vectorScale = 1;
vectorSymmetry = vwr.getBoolean(T.vectorsymmetry);
@@ -115,14 +121,14 @@
needTranslucent = true;
continue;
}
- renderVector(atom);
+ renderVector(atom, vib);
if (vectorSymmetry) {
if (vibTemp == null)
vibTemp = new Vibration();
vibTemp.setT(vib);
vibTemp.scale(-1);
transform(mads[i], atom, vibTemp, null);
- renderVector(atom);
+ renderVector(atom, vib);
}
}
if (haveModulations)
@@ -133,21 +139,22 @@
JmolModulationSet mod = ms.getModulation(i);
if (mod == null)
continue;
+ if (!g3d.setC(Shape.getColix(colixes, i, atom))) {
+ needTranslucent = true;
+ continue;
+ }
// now we focus on modulations
// this may involve a modulated atom or a spin modulation
if (!transform(mads[i], atom, null, mod))
continue;
- if (!g3d.setC(Shape.getColix(colixes, i, atom))) {
- needTranslucent = true;
- continue;
- }
- renderVector(atom);
+ renderVector(atom, null);
}
return needTranslucent;
}
- private boolean transform(short mad, Atom atom, Vibration vib,
JmolModulationSet mod2) {
+ private boolean transform(short mad, Atom atom, Vibration vib,
+ JmolModulationSet mod2) {
boolean isMod = (vib == null || vib.modDim >= 0);
boolean isSpin = (!isMod && vib.modDim == Vibration.TYPE_SPIN);
if (vib == null)
@@ -188,15 +195,15 @@
headOffsetVector.scale(headScale / headOffsetVector.length());
} else if (vectorsCentered || isSpin) {
standardVector = false;
- // Vibration v;
- // if (mod2 == null || !mod2.isEnabled()) {
- // v = vib;
-// } else {
-// v = vibTemp;
-// vibTemp.set(0, 0, 0);
-// v.setTempPoint(vibTemp, null, 1, vwr.g.modulationScale);
-// vwr.tm.getVibrationPoint(vib, v, Float.NaN);
-// }
+ // Vibration v;
+ // if (mod2 == null || !mod2.isEnabled()) {
+ // v = vib;
+ // } else {
+ // v = vibTemp;
+ // vibTemp.set(0, 0, 0);
+ // v.setTempPoint(vibTemp, null, 1, vwr.g.modulationScale);
+ // vwr.tm.getVibrationPoint(vib, v, Float.NaN);
+ // }
pointVectorEnd.scaleAdd2(0.5f * vectorScale, vib, ptTemp);
pointVectorStart.scaleAdd2(-0.5f * vectorScale, vib, ptTemp);
} else {
@@ -212,6 +219,7 @@
tm.transformPtScrT3(pointArrowHead, screenArrowHead);
}
}
+
if (!standardVector) {
tm.transformPtScrT3(pointVectorEnd, screenVectorEnd);
tm.transformPtScrT3(pointVectorStart, screenVectorStart);
@@ -226,10 +234,30 @@
headWidthPixels = diameter << 1;
if (headWidthPixels < diameter + 2)
headWidthPixels = diameter + 2;
+
return true;
}
- private void renderVector(Atom atom) {
+ private void renderVector(Atom atom, Vibration vib) {
+ if (vib != null && vectorTrace > 0) {// show trace
+ if (ptTemp4 == null) {
+ ptTemp3 = new P3();
+ ptTemp4 = new P3();
+ ptTemp2 = new P3();
+ }
+ int d = Math.max(1, diameter >> 2);
+ P3[] pts = vib.addTracePt(vectorTrace, pointVectorEnd);
+ tm.transformPtScrT3(atom, ptTemp4);
+ if (pts != null)
+ for (int i = pts.length, p = vectorTrace; --i >= 0;) {
+ P3 pt = pts[--p];
+ if (pt == null)
+ break;
+ tm.transformPtScrT3(pt, ptTemp2);
+ g3d.fillCylinderBits(GData.ENDCAPS_FLAT, d, ptTemp4, ptTemp2);
+ }
+ }
+
if (drawShaft) {
pTemp3.set(atom.sX, atom.sY, atom.sZ);
if (standardVector)
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2016-03-22 18:50:47 UTC
(rev 21016)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2016-03-23 04:35:05 UTC
(rev 21017)
@@ -4590,7 +4590,7 @@
} else if (!isData) {
if (localName != null)
localName = vwr.fm.getFilePath(localName, false, false);
- if (!filename.equals("string") && !filename.equals("String[]"))
+ if (!filename.equals("String[]"))
loadScript.append("/*file*/").append(
(localName != null ? PT.esc(localName) : "$FILENAME$"));
}
@@ -7885,6 +7885,9 @@
break;
case 3:
switch (tokAt(1)) {
+ case T.trace:
+ setIntProperty("vectorTrace", intParameterRange(2, 0, 20));
+ return;
case T.scale:
if (!Float.isNaN(value = floatParameterRange(2, -100, 100)))
setFloatProperty("vectorScale", value);
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2016-03-22 18:50:47 UTC (rev
21016)
+++ trunk/Jmol/src/org/jmol/script/T.java 2016-03-23 04:35:05 UTC (rev
21017)
@@ -934,6 +934,7 @@
public final static int strandcountformeshribbon = intparam | 52;
public final static int strandcountforstrands = intparam | 54;
public final static int strutspacing = intparam | 56;
+ public final static int vectortrail = intparam | 57;
public final static int zdepth = intparam | 58;
public final static int zslab = intparam | 60;
public final static int zshadepower = intparam | 62;
@@ -1081,9 +1082,9 @@
public final static int usenumberlocalization = booleanparam | 195;
public final static int vectorscentered = booleanparam | 196;
public final static int vectorsymmetry = booleanparam | 197;
- public final static int waitformoveto = booleanparam | 198;
- public final static int windowcentered = booleanparam | 199;
- public final static int wireframerotation = booleanparam | 200;
+ public final static int waitformoveto = booleanparam | 199;
+ public final static int windowcentered = booleanparam | 200;
+ public final static int wireframerotation = booleanparam | 201;
public final static int zerobasedxyzrasmol = booleanparam | 202;
public final static int zoomenabled = booleanparam | 204;
public final static int zoomheight = booleanparam | 206;
@@ -2435,6 +2436,7 @@
"vectorScale",
"vectorsCentered",
"vectorSymmetry",
+ "vectorTrail",
"vibrationPeriod",
"vibrationScale",
"visualRange",
@@ -3472,6 +3474,7 @@
vectorscale, // "vectorScale"
vectorscentered, // "vectorsCenered"
vectorsymmetry, // "vectorSymmetry"
+ vectortrail, // "vectorTrail"
vibrationperiod, // "vibrationPeriod"
vibrationscale, // "vibrationScale"
visualrange, // "visualRange"
Modified: trunk/Jmol/src/org/jmol/util/Vibration.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Vibration.java 2016-03-22 18:50:47 UTC (rev
21016)
+++ trunk/Jmol/src/org/jmol/util/Vibration.java 2016-03-23 04:35:05 UTC (rev
21017)
@@ -2,6 +2,7 @@
import java.util.Map;
+import javajs.util.P3;
import javajs.util.T3;
import javajs.util.V3;
@@ -88,4 +89,32 @@
return Integer.MIN_VALUE;
}
+ public boolean showTrace;
+ private P3[] trace = null;
+ public int tracePt;
+
+ public void startTrace(int n) {
+ trace = new P3[n];
+ tracePt = n;
+ }
+
+ public P3[] addTracePt(int n, Point3fi ptNew) {
+ if (ptNew == null || trace == null || n == 0 || n > trace.length)
+ startTrace(n);
+ if (ptNew != null && n > 2) {
+ if (--tracePt <= 0) {
+ P3 p0 = trace[trace.length - 1];
+ for (int i = trace.length; --i >= 1;)
+ trace[i] = trace[i-1];
+ trace[1] = p0;
+ tracePt = 1;
+ }
+ P3 p = trace[tracePt];
+ if (p == null)
+ p = trace[tracePt] = new P3();
+ p.setT(ptNew);
+ }
+ return trace;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2016-03-22 18:50:47 UTC
(rev 21016)
+++ trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2016-03-23 04:35:05 UTC
(rev 21017)
@@ -379,6 +379,7 @@
setB("vectorsCentered", vectorsCentered);
setF("vectorScale", vectorScale);
setB("vectorSymmetry", vectorSymmetry);
+ setI("vectorTrail", vectorTrail);
setF("vibrationPeriod", vibrationPeriod);
setF("vibrationScale", vibrationScale);
setB("waitForMoveTo", waitForMoveTo);
@@ -629,6 +630,7 @@
float vectorScale = 1f;
boolean vectorSymmetry = false; // Jmol 12.3.2
boolean vectorsCentered = false; // Jmol 14.1.14
+ int vectorTrail = 0; // Jmol 14.4.4
float vibrationPeriod = 1f;
float vibrationScale = 1f;
boolean wireframeRotation = false;
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2016-03-22 18:50:47 UTC (rev
21016)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2016-03-23 04:35:05 UTC (rev
21017)
@@ -68,6 +68,7 @@
"map",
"http://www.ebi.ac.uk/pdbe/api/%TYPE/%FILE?pretty=false&metadata=true";,
"rna3d", "http://rna.bgsu.edu/rna3dhub/%TYPE/download/%FILE";,
"aflow",
"http://aflowlib.mems.duke.edu/users/jmolers/binary_new/%FILE.aflow_binary";,
+ "magndata", "http://webbdcrista1.ehu.es/magndata/mcif/%FILE.mcif";,
// _#CHANGEABLE_ flag indicates that the loaded file should be saved in
any state in full
// ' at start indicates a Jmol script evaluation
"ams", "'http://rruff.geo.arizona.edu/AMS/viewJmol.php?'+(0+'%file'==0?
'mineral':('%file'.length==7? 'amcsd':'id'))+'=%file&action=showcif#_DOCACHE_'",
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-22 18:50:47 UTC
(rev 21016)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-23 04:35:05 UTC
(rev 21017)
@@ -69,6 +69,21 @@
Jmol.___JmolVersion="14.5.4_2016.03.23"
+new feature: load =magndata/1.1.37
+ -- links to the MAGNDATA database at http://webbdcrista1.ehu.es/magndata
+ -- "magndata", "http://webbdcrista1.ehu.es/magndata/mcif/%FILE.mcif";,
+
+new feature: set vectorTrail n
+ -- adds a trail onto a modulating vector (as for an incommensurate magnetic
spin)
+ -- n trails are made, typically in a fan-like pattern that trails the
spinning vector
+ load =magndata/1.1.37
+ set vectortrace 20
+ set vibrationperiod 2
+ vibration on
+
+bug fix: saving a state after using LOAD "" (empty quotes)
+ after pasting data directly into the application creates an
unreadable state
+
new feature: unitcell ON adds #nnn (international table number) to cell
description if found
bug fix: {*}.find("CHEMICAL","NAMES") only reports one name.
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-03-22 18:50:47 UTC (rev
21016)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-03-23 04:35:05 UTC (rev
21017)
@@ -1884,7 +1884,7 @@
htParams.put(
"loadScript",
loadScript = new SB().append(PT.rep(loadScript.toString(),
- "$FILENAME$", "data \"model inline\"\n" + strModel
+ "/*file*/$FILENAME$", "/*data*/data \"model inline\"\n" +
strModel
+ "end \"model inline\"")));
}
if (strModel != null) {
@@ -5038,6 +5038,8 @@
return g.smallMoleculeMaxAtoms;
case T.strutspacing:
return g.strutSpacing;
+ case T.vectortrail:
+ return g.vectorTrail;
}
Logger.error("viewer.getInt(" + T.nameOf(tok) + ") - not listed");
return 0;
@@ -5774,6 +5776,9 @@
case T.scriptreportinglevel:
value = eval.setStatic(tok, value);
break;
+ case T.vectortrail:
+ g.vectorTrail = value;
+ break;
case T.bondingversion:
// 14.1.11
value = (value == 0 ? Elements.RAD_COV_IONIC_OB1_100_1
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