Revision: 20134
http://sourceforge.net/p/jmol/code/20134
Author: hansonr
Date: 2014-11-26 04:46:18 +0000 (Wed, 26 Nov 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.10_2014.11.27"
FEATURE CHANGE: undocumented omission of "CUTOFF" keyword prior to number in
ISOSURFACE command disallowed
new feature: isosurface LATTICE {i j k} FIXED
-- creates an isosurface from periodic volumetric data
with the specified number of unit cells
-- "fixed" in the sense that the operation is at load time
not at rendering, allowing slabbing and use of WITHIN
new feature: isosurface + x.x ....
-- for periodic lattices only
-- expands one unit cell by x.x in fractional coordinates
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java
trunk/Jmol/src/org/jmol/jvxl/data/JvxlData.java
trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java 2014-11-26 04:04:14 UTC
(rev 20133)
+++ trunk/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java 2014-11-26 04:46:18 UTC
(rev 20134)
@@ -308,8 +308,8 @@
if (!jvxlData.allowVolumeRender)
addAttrib(attribs, "\n allowVolumeRender", "false");
if (jvxlData.jvxlPlane == null || vertexDataOnly) {
- if (jvxlData.processLattice != null && !vertexDataOnly)
- addAttrib(attribs, "\n processLattice", "" + jvxlData.processLattice);
+ if (jvxlData.fixedLattice != null && !vertexDataOnly)
+ addAttrib(attribs, "\n fixedLattice", "" + jvxlData.fixedLattice);
if (jvxlData.isContoured) {
addAttrib(attribs, "\n contoured", "true");
addAttrib(attribs, "\n colorMapped", "true");
Modified: trunk/Jmol/src/org/jmol/jvxl/data/JvxlData.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/data/JvxlData.java 2014-11-26 04:04:14 UTC
(rev 20133)
+++ trunk/Jmol/src/org/jmol/jvxl/data/JvxlData.java 2014-11-26 04:46:18 UTC
(rev 20134)
@@ -173,7 +173,7 @@
public boolean allowVolumeRender;
public float voxelVolume;
public P3 mapLattice;
- public P3 processLattice;
+ public P3 fixedLattice;
public String baseColor;
public void clear() {
@@ -196,7 +196,7 @@
msg = "";
nPointsX = 0;
nVertexColors = 0;
- processLattice = null;
+ fixedLattice = null;
slabInfo = null;
slabValue = Integer.MIN_VALUE;
thisSet = Integer.MIN_VALUE;
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java 2014-11-26
04:04:14 UTC (rev 20133)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java 2014-11-26
04:46:18 UTC (rev 20134)
@@ -297,9 +297,9 @@
params.thePlane = null;
surfaceDataCount = parseIntStr(XmlReader.getXmlAttrib(data,
"nSurfaceInts"));
edgeDataCount = parseIntStr(XmlReader.getXmlAttrib(data,
"nBytesUncompressedEdgeData"));
- s = XmlReader.getXmlAttrib(data, "processLattice");
+ s = XmlReader.getXmlAttrib(data, "fixedLattice");
if (s.indexOf("{") >= 0)
- jvxlData.processLattice = (P3) Escape.uP(s);
+ jvxlData.fixedLattice = (P3) Escape.uP(s);
}
excludedVertexCount = parseIntStr(XmlReader.getXmlAttrib(data,
"nExcludedVertexes"));
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-11-26 04:04:14 UTC
(rev 20133)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-11-26 04:46:18 UTC
(rev 20134)
@@ -2876,7 +2876,7 @@
P3 pt;
P4 plane = null;
P3 lattice = null;
- boolean processLattice = false;
+ boolean fixLattice = false;
P3[] pts;
int color = 0;
String str = null;
@@ -3724,14 +3724,9 @@
sbCommand.append(" ").appendO(propertyValue);
}
break;
- case T.decimal:
- case T.integer:
- case T.plus:
case T.cutoff:
sbCommand.append(" cutoff ");
- if (eval.theTok == T.cutoff)
- i++;
- if (tokAt(i) == T.plus) {
+ if (tokAt(++i) == T.plus) {
propertyName = "cutoffPositive";
propertyValue = Float.valueOf(cutoff = floatParameter(++i));
sbCommand.append("+").appendO(propertyValue);
@@ -4272,13 +4267,12 @@
case T.lattice:
if (iShape != JC.SHAPE_ISOSURFACE)
invArg();
- if (tokAt(i + 1) == T.plus) {
- i += 2;
+ if (tokAt(++i) == T.plus) {
propertyName = "extendLattice";
- propertyValue = Float.valueOf(floatParameter(i));
+ propertyValue = Float.valueOf(floatParameter(++i));
sbCommand.append(" lattice + " + propertyValue);
} else {
- pt = getPoint3f(i + 1, false);
+ pt = getPoint3f(i, false);
i = eval.iToken;
if (pt.x <= 0 || pt.y <= 0 || pt.z <= 0)
break;
@@ -4291,9 +4285,9 @@
propertyValue = pt;
} else {
lattice = pt;
- if (tokAt(i + 1) == T.on) {
- sbCommand.append(" true");
- processLattice = true;
+ if (tokAt(i + 1) == T.fixed) {
+ sbCommand.append(" fixed");
+ fixLattice = true;
i++;
}
}
@@ -4408,8 +4402,8 @@
}
if (lattice != null) { // before MAP, this is a display option
setShapeProperty(iShape, "lattice", lattice);
- if (processLattice)
- setShapeProperty(iShape, "processLattice", Boolean.TRUE);
+ if (fixLattice)
+ setShapeProperty(iShape, "fixLattice", Boolean.TRUE);
}
if (symops != null) // before MAP, this is a display option
setShapeProperty(iShape, "symops", symops);
Modified: trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2014-11-26
04:04:14 UTC (rev 20133)
+++ trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2014-11-26
04:46:18 UTC (rev 20134)
@@ -487,9 +487,9 @@
return;
}
- if ("processLattice" == propertyName) {
+ if ("fixLattice" == propertyName) {
if (thisMesh != null)
- thisMesh.processLattice(vwr);
+ thisMesh.fixLattice(vwr);
return;
}
@@ -1441,9 +1441,9 @@
if (!thisMesh.isMerged) {
thisMesh.initialize(sg.isFullyLit() ? T.fullylit
: T.frontlit, null, sg.getPlane());
- if (jvxlData.processLattice != null) {
- thisMesh.lattice = jvxlData.processLattice;
- thisMesh.processLattice(vwr);
+ if (jvxlData.fixedLattice != null) {
+ thisMesh.lattice = jvxlData.fixedLattice;
+ thisMesh.fixLattice(vwr);
}
return;
Modified: trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2014-11-26
04:04:14 UTC (rev 20133)
+++ trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2014-11-26
04:46:18 UTC (rev 20134)
@@ -922,12 +922,12 @@
spanningVectors, true, null)) != null ? unitCell : null);
}
- void processLattice(Viewer vwr) {
+ void fixLattice(Viewer vwr) {
if (getUnitCell(vwr) == null)
return;
P3i minXYZ = new P3i();
P3i maxXYZ = P3i.new3((int) lattice.x, (int) lattice.y, (int) lattice.z);
- jvxlData.processLattice = lattice;
+ jvxlData.fixedLattice = lattice;
lattice = null;
unitCell.setMinMaxLatticeParameters(minXYZ, maxXYZ);
int nCells = (maxXYZ.x - minXYZ.x) * (maxXYZ.y - minXYZ.y)
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-26 04:04:14 UTC
(rev 20133)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-26 04:46:18 UTC
(rev 20134)
@@ -17,7 +17,15 @@
Jmol.___JmolVersion="14.3.10_2014.11.27"
-new feature: isosurface LATTICE + x.x ....
+FEATURE CHANGE: undocumented omission of "CUTOFF" keyword prior to number in
ISOSURFACE command disallowed
+
+new feature: isosurface LATTICE {i j k} FIXED
+ -- creates an isosurface from periodic volumetric data
+ with the specified number of unit cells
+ -- "fixed" in the sense that the operation is at load time
+ not at rendering, allowing slabbing and use of WITHIN
+
+new feature: isosurface + x.x ....
-- for periodic lattices only
-- expands one unit cell by x.x in fractional coordinates
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