Revision: 20122
http://sourceforge.net/p/jmol/code/20122
Author: hansonr
Date: 2014-11-23 23:25:34 +0000 (Sun, 23 Nov 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.2.9_2014.11.23"
bug fix: isosurface slab plane -xy not recognizing "-"
bug fix: PNGJ writing broken
bug fix: VASP CHGCAR reader not recognized for primitive cell
bug fix: Euler ZYZ and ZXZ for quaternion({0 0 1},theta) where theta < 0 in
error
Modified Paths:
--------------
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
Modified: branches/v14_2/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java
2014-11-23 23:25:08 UTC (rev 20121)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java
2014-11-23 23:25:34 UTC (rev 20122)
@@ -104,12 +104,12 @@
bsMyIgnored = params.bsIgnore;
if (params.volumeData != null) {
setVolumeDataV(params.volumeData);
- setBBox(volumeData.volumetricOrigin);
+ setBBox(volumeData.volumetricOrigin, 0);
ptV.setT(volumeData.volumetricOrigin);
for (int i = 0; i < 3; i++)
ptV.scaleAdd2(volumeData.voxelCounts[i] - 1,
volumeData.volumetricVectors[i], ptV);
- setBBox(ptV);
+ setBBox(ptV, 0);
}
havePlane = (params.thePlane != null);
if (havePlane)
@@ -265,11 +265,11 @@
Logger.info(myAtomCount + " atoms will be used in the surface
calculation");
if (myAtomCount == 0) {
- setBBox(P3.new3(10, 10, 10));
- setBBox(P3.new3(-10, -10, -10));
+ setBBox(P3.new3(10, 10, 10), 0);
+ setBBox(P3.new3(-10, -10, -10), 0);
}
for (int i = 0; i < myAtomCount; i++)
- setBBox(atomXyz[i]);
+ setBBox(atomXyz[i], getRadii ? atomRadius[i] + 0.5f : 0);
if (!Float.isNaN(params.scale)) {
V3 v = V3.newVsub(xyzMax, xyzMin);
v.scale(0.5f);
Modified: branches/v14_2/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
2014-11-23 23:25:08 UTC (rev 20121)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
2014-11-23 23:25:34 UTC (rev 20122)
@@ -1094,12 +1094,12 @@
meshData.setBox(xyzMin, xyzMax);
}
- protected void setBBox(T3 pt) {
+ protected void setBBox(T3 pt, float margin) {
if (xyzMin == null) {
xyzMin = P3.new3(Float.MAX_VALUE, Float.MAX_VALUE, Float.MAX_VALUE);
xyzMax = P3.new3(-Float.MAX_VALUE, -Float.MAX_VALUE, -Float.MAX_VALUE);
}
- BoxInfo.addPoint(pt, xyzMin, xyzMax, 0);
+ BoxInfo.addPoint(pt, xyzMin, xyzMax, margin);
}
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