Revision: 20120
http://sourceforge.net/p/jmol/code/20120
Author: hansonr
Date: 2014-11-23 22:45:58 +0000 (Sun, 23 Nov 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.2.9_2014.11.23"
released as Jmol 14.3.9 and Jmol 14.2.9
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/io/JmolUtil.java
branches/v14_2/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java
branches/v14_2/Jmol/src/org/jmol/jvxl/data/JvxlData.java
branches/v14_2/Jmol/src/org/jmol/jvxl/data/MeshData.java
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
branches/v14_2/Jmol/src/org/jmol/render/MeshRenderer.java
branches/v14_2/Jmol/src/org/jmol/script/ScriptParam.java
branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java
branches/v14_2/Jmol/src/org/jmol/shape/Mesh.java
branches/v14_2/Jmol/src/org/jmol/shapesurface/Isosurface.java
branches/v14_2/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
branches/v14_2/Jmol/src/org/jmol/util/BoxInfo.java
branches/v14_2/Jmol/src/org/jmol/util/MeshSurface.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_2/Jmol/src/org/jmol/viewer/OutputManager.java
branches/v14_2/Jmol/src/org/jmol/viewer/StatusManager.java
Modified: branches/v14_2/Jmol/src/org/jmol/io/JmolUtil.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/io/JmolUtil.java 2014-11-23 22:35:24 UTC
(rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/io/JmolUtil.java 2014-11-23 22:45:58 UTC
(rev 20120)
@@ -366,8 +366,9 @@
int nAtoms = PT.parseInt(line3);
if (nAtoms == Integer.MIN_VALUE)
return (line3.indexOf("+") == 0 ? "Jvxl+" : null);
- if (line3.indexOf(".") > 0)
- return (line3.length() >= 60 || PT.getTokens(line3).length != 3 ? null :
"VaspChgcar"); // M40 files are > 60 char
+ tokens = PT.getTokens(line3);
+ if (tokens[0].indexOf(".") > 0)
+ return (line3.length() >= 60 || tokens.length != 3 ? null :
"VaspChgcar"); // M40 files are > 60 char
if (nAtoms >= 0)
return "Cube"; //Can't be a Jvxl file;
nAtoms = -nAtoms;
Modified: branches/v14_2/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java 2014-11-23
22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java 2014-11-23
22:45:58 UTC (rev 20120)
@@ -308,6 +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.isContoured) {
addAttrib(attribs, "\n contoured", "true");
addAttrib(attribs, "\n colorMapped", "true");
Modified: branches/v14_2/Jmol/src/org/jmol/jvxl/data/JvxlData.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/data/JvxlData.java 2014-11-23
22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/data/JvxlData.java 2014-11-23
22:45:58 UTC (rev 20120)
@@ -172,6 +172,7 @@
public boolean allowVolumeRender;
public float voxelVolume;
public P3 mapLattice;
+ public P3 processLattice;
public String baseColor;
public void clear() {
@@ -190,6 +191,7 @@
contourColors = null;
isSlabbable = false;
mapLattice = null;
+ processLattice = null;
meshColor = null;
nPointsX = 0;
nVertexColors = 0;
Modified: branches/v14_2/Jmol/src/org/jmol/jvxl/data/MeshData.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/data/MeshData.java 2014-11-23
22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/data/MeshData.java 2014-11-23
22:45:58 UTC (rev 20120)
@@ -364,5 +364,6 @@
vvs[i] = Float.NaN;
}
+
}
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 22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/AtomDataReader.java
2014-11-23 22:45:58 UTC (rev 20120)
@@ -104,12 +104,12 @@
bsMyIgnored = params.bsIgnore;
if (params.volumeData != null) {
setVolumeDataV(params.volumeData);
- setBBox(volumeData.volumetricOrigin, 0);
+ setBBox(volumeData.volumetricOrigin);
ptV.setT(volumeData.volumetricOrigin);
for (int i = 0; i < 3; i++)
ptV.scaleAdd2(volumeData.voxelCounts[i] - 1,
volumeData.volumetricVectors[i], ptV);
- setBBox(ptV, 0);
+ setBBox(ptV);
}
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), 0);
- setBBox(P3.new3(-10, -10, -10), 0);
+ setBBox(P3.new3(10, 10, 10));
+ setBBox(P3.new3(-10, -10, -10));
}
for (int i = 0; i < myAtomCount; i++)
- setBBox(atomXyz[i], getRadii ? atomRadius[i] + 0.5f : 0);
+ setBBox(atomXyz[i]);
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/CastepDensityReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
2014-11-23 22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
2014-11-23 22:45:58 UTC (rev 20120)
@@ -95,6 +95,7 @@
@Override
protected void getPeriodicVoxels() throws Exception {
+ // no downsampling (yet), because CASTEP writes x, y, z info.
for (int i = 0; i < nFilePoints; i++) {
int x = parseIntStr(line) - 1;
int y = parseInt() - 1;
Modified: branches/v14_2/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
2014-11-23 22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
2014-11-23 22:45:58 UTC (rev 20120)
@@ -236,6 +236,7 @@
params.nContours = (haveContourData ? nContourData : nContoursRead);
//TODO ? params.contourFromZero = false; // MEP data to complete the
plane
}
+
jvxlData.nVertexColors = parseIntStr(XmlReader.getXmlAttrib(data,
"nVertexColors"));
params.isBicolorMap = XmlReader.getXmlAttrib(data,
"bicolorMap").equals("true");
if (params.isBicolorMap) {
@@ -296,6 +297,10 @@
params.thePlane = null;
surfaceDataCount = parseIntStr(XmlReader.getXmlAttrib(data,
"nSurfaceInts"));
edgeDataCount = parseIntStr(XmlReader.getXmlAttrib(data,
"nBytesUncompressedEdgeData"));
+ s = XmlReader.getXmlAttrib(data, "processLattice");
+ if (s.indexOf("{") >= 0)
+ jvxlData.processLattice = (P3) Escape.uP(s);
+
}
excludedVertexCount = parseIntStr(XmlReader.getXmlAttrib(data,
"nExcludedVertexes"));
excludedTriangleCount = parseIntStr(XmlReader.getXmlAttrib(data,
"nExcludedTriangles"));
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 22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
2014-11-23 22:45:58 UTC (rev 20120)
@@ -212,6 +212,7 @@
protected boolean isXLowToHigh = false; //can be overridden in some readers
by --progressive
private float assocCutoff = 0.3f;
protected boolean isQuiet;
+ protected boolean isPeriodic;
boolean vertexDataOnly;
boolean hasColorData;
@@ -1088,20 +1089,17 @@
private void setBBoxAll() {
if (meshDataServer != null)
meshDataServer.fillMeshData(meshData, MeshData.MODE_GET_VERTICES, null);
- xyzMin = null;
- for (int i = 0; i < meshData.vc; i++) {
- T3 p = meshData.vs[i];
- if (!Float.isNaN(p.x))
- setBBox(p, 0);
- }
+ xyzMin = new P3();
+ xyzMax = new P3();
+ meshData.setBox(xyzMin, xyzMax);
}
- protected void setBBox(T3 pt, float margin) {
+ protected void setBBox(T3 pt) {
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, margin);
+ BoxInfo.addPoint(pt, xyzMin, xyzMax, 0);
}
/**
Modified: branches/v14_2/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
2014-11-23 22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
2014-11-23 22:45:58 UTC (rev 20120)
@@ -40,8 +40,9 @@
void init2(SurfaceGenerator sg, BufferedReader br) {
init2VFR(sg, br);
isAngstroms = true;
+ isPeriodic = true;
+ isProgressive = false; // for now
nSurfaces = 1;
- canDownsample = isProgressive = false; // for now
}
// pt
@@ -71,7 +72,7 @@
@Override
protected void readParameters() throws Exception {
jvxlFileHeaderBuffer = new SB();
- jvxlFileHeaderBuffer.append("Vasp CHGCAR format\n");
+ jvxlFileHeaderBuffer.append("Vasp CHGCAR format\n\n\n");
rd(); // atoms
float scale = parseFloatStr(rd());
float[] data = new float[15];
@@ -108,15 +109,30 @@
@Override
protected void getPeriodicVoxels() throws Exception {
+ // we are not reading the final periodic values
int ni = voxelCounts[0] - 1;
int nj = voxelCounts[1] - 1;
int nk = voxelCounts[2] - 1;
- for (int i = 0; i < ni; i++)
- for (int j = 0; j < nj; j++)
- for (int k = 0; k < nk; k++)
+ boolean downSampling = (nSkipX > 0);
+ for (int i = 0; i < ni; i++) {
+ for (int j = 0; j < nj; j++) {
+ for (int k = 0; k < nk; k++) {
voxelData[i][j][k] = recordData(nextVoxel());
+ if (downSampling)
+ for (int m = nSkipX; --m >= 0;)
+ nextVoxel();
+ }
+ if (downSampling)
+ for (int m = nSkipY; --m >= 0;)
+ nextVoxel();
+ }
+ if (downSampling)
+ for (int m = nSkipZ; --m >= 0;)
+ nextVoxel();
+ }
}
+
@Override
protected void readSkip() throws Exception {
// n/a
Modified: branches/v14_2/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
2014-11-23 22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
2014-11-23 22:45:58 UTC (rev 20120)
@@ -49,7 +49,7 @@
protected int nSurfaces;
protected boolean isAngstroms;
protected boolean canDownsample;
- private int[] downsampleRemainders;
+ protected int[] downsampleRemainders;
private boolean preProcessPlanes;
private int nData;
private boolean readerClosed;
@@ -145,6 +145,10 @@
int n = voxelCounts[i];
downsampleRemainders[i] = n % downsampleFactor;
voxelCounts[i] /= downsampleFactor;
+ if (isPeriodic) {
+ voxelCounts[i]++;
+ downsampleRemainders[i]--;
+ }
volumetricVectors[i].scale(downsampleFactor);
Logger.info("downsampling axis " + (i + 1) + " from " + n + " to "
+ voxelCounts[i]);
@@ -191,7 +195,7 @@
}
protected int downsampleFactor;
- private int nSkipX, nSkipY, nSkipZ;
+ protected int nSkipX, nSkipY, nSkipZ;
void initializeSurfaceData() {
downsampleFactor = params.downsampleFactor;
@@ -201,9 +205,9 @@
if (canDownsample && downsampleFactor > 0) {
nSkipX = downsampleFactor - 1;
nSkipY = downsampleRemainders[2] + (downsampleFactor - 1)
- * (nSkipZ = (nPointsZ * downsampleFactor + downsampleRemainders[2]));
+ * (nSkipZ = ((nPointsZ - (isPeriodic ? 1 : 0)) * downsampleFactor +
downsampleRemainders[2]));
nSkipZ = downsampleRemainders[1] * nSkipZ + (downsampleFactor - 1)
- * nSkipZ * (nPointsY * downsampleFactor + downsampleRemainders[1]);
+ * nSkipZ * ((nPointsY - (isPeriodic ? 1 : 0)) * downsampleFactor +
downsampleRemainders[1]);
}
if (params.thePlane != null) {
Modified: branches/v14_2/Jmol/src/org/jmol/render/MeshRenderer.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/render/MeshRenderer.java 2014-11-23
22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/render/MeshRenderer.java 2014-11-23
22:45:58 UTC (rev 20120)
@@ -97,54 +97,51 @@
if (!doRender)
return mesh.title != null;
latticeOffset.set(0, 0, 0);
- if (mesh.lattice == null && mesh.symops == null || mesh.modelIndex < 0) {
+ if (mesh.modelIndex < 0
+ || mesh.lattice == null && mesh.symops == null) {
for (int i = vertexCount; --i >= 0;)
if (vertices[i] != null)
tm.transformPtScr(vertices[i], screens[i]);
render2(isExport);
} else {
P3 vTemp = new P3();
- SymmetryInterface unitcell;
- if ((unitcell = mesh.unitCell) == null
- && (unitcell = vwr.ms.am[mesh.modelIndex].biosymmetry) == null
- && (unitcell = vwr.getModelUnitCell(mesh.modelIndex)) == null)
- unitcell = mesh.getUnitCell(vwr);
- if (mesh.symops != null) {
- if (mesh.symopNormixes == null)
- mesh.symopNormixes = AU.newShort2(mesh.symops.length);
- P3[] verticesTemp = null;
- int max = mesh.symops.length;
- short c = mesh.colix;
- for (int j = max; --j >= 0;) {
- M4 m = mesh.symops[j];
- if (m == null)
- continue;
- if (mesh.colorType == T.symop)
- mesh.colix = mesh.symopColixes[j];
- short[] normals = mesh.symopNormixes[j];
- boolean needNormals = (normals == null);
- verticesTemp = (needNormals ? new P3[vertexCount] : null);
- for (int i = vertexCount; --i >= 0;) {
- vTemp.setT(vertices[i]);
- unitcell.toFractional(vTemp, true);
- m.rotTrans(vTemp);
- unitcell.toCartesian(vTemp, true);
- tm.transformPtScr(vTemp, screens[i]);
- if (needNormals) {
- verticesTemp[i] = vTemp;
- vTemp = new P3();
+ SymmetryInterface unitcell = mesh.getUnitCell(vwr);
+ if (unitcell != null) {
+ if (mesh.symops != null) {
+ if (mesh.symopNormixes == null)
+ mesh.symopNormixes = AU.newShort2(mesh.symops.length);
+ P3[] verticesTemp = null;
+ int max = mesh.symops.length;
+ short c = mesh.colix;
+ for (int j = max; --j >= 0;) {
+ M4 m = mesh.symops[j];
+ if (m == null)
+ continue;
+ if (mesh.colorType == T.symop)
+ mesh.colix = mesh.symopColixes[j];
+ short[] normals = mesh.symopNormixes[j];
+ boolean needNormals = (normals == null);
+ verticesTemp = (needNormals ? new P3[vertexCount] : null);
+ for (int i = vertexCount; --i >= 0;) {
+ vTemp.setT(vertices[i]);
+ unitcell.toFractional(vTemp, true);
+ m.rotTrans(vTemp);
+ unitcell.toCartesian(vTemp, true);
+ tm.transformPtScr(vTemp, screens[i]);
+ if (needNormals) {
+ verticesTemp[i] = vTemp;
+ vTemp = new P3();
+ }
}
+ if (needNormals)
+ normixes = mesh.symopNormixes[j] = mesh.setNormixes(mesh
+ .getNormals(verticesTemp, null));
+ else
+ normixes = mesh.normixes = mesh.symopNormixes[j];
+ render2(isExport);
}
- if (needNormals)
- normixes = mesh.symopNormixes[j] =
mesh.setNormixes(mesh.getNormals(
- verticesTemp, null));
- else
- normixes = mesh.normixes = mesh.symopNormixes[j];
- render2(isExport);
- }
- mesh.colix = c;
- } else {
- if (unitcell != null) {
+ mesh.colix = c;
+ } else {
P3i minXYZ = new P3i();
P3i maxXYZ = P3i.new3((int) mesh.lattice.x, (int) mesh.lattice.y,
(int) mesh.lattice.z);
Modified: branches/v14_2/Jmol/src/org/jmol/script/ScriptParam.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/ScriptParam.java 2014-11-23
22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/script/ScriptParam.java 2014-11-23
22:45:58 UTC (rev 20120)
@@ -288,12 +288,11 @@
case T.string:
String str = paramAsStr(i);
if (str.equalsIgnoreCase("xy"))
- return P4.new4(0, 0, 1, 0);
- if (str.equalsIgnoreCase("xz"))
- return P4.new4(0, 1, 0, 0);
- if (str.equalsIgnoreCase("yz"))
- return P4.new4(1, 0, 0, 0);
- iToken += 2;
+ plane = P4.new4(0, 0, isNegated ? -1 : 1, 0);
+ else if (str.equalsIgnoreCase("xz"))
+ plane = P4.new4(0, isNegated ? -1 : 1, 0, 0);
+ else if (str.equalsIgnoreCase("yz"))
+ plane = P4.new4(isNegated ? -1 : 1, 0, 0, 0);
break;
case T.leftbrace:
case T.point3f:
Modified: branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-11-23
22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-11-23
22:45:58 UTC (rev 20120)
@@ -2876,6 +2876,7 @@
P3 pt;
P4 plane = null;
P3 lattice = null;
+ boolean processLattice = false;
P3[] pts;
int color = 0;
String str = null;
@@ -4276,6 +4277,11 @@
propertyValue = pt;
} else {
lattice = pt;
+ if (tokAt(i + 1) == T.on) {
+ sbCommand.append(" true");
+ processLattice = true;
+ i++;
+ }
}
break;
default:
@@ -4385,8 +4391,11 @@
sbCommand.append(" mesh nofill frontOnly");
}
}
- if (lattice != null) // before MAP, this is a display option
+ if (lattice != null) { // before MAP, this is a display option
setShapeProperty(iShape, "lattice", lattice);
+ if (processLattice)
+ setShapeProperty(iShape, "processLattice", Boolean.TRUE);
+ }
if (symops != null) // before MAP, this is a display option
setShapeProperty(iShape, "symops", symops);
if (isFrontOnly)
Modified: branches/v14_2/Jmol/src/org/jmol/shape/Mesh.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/shape/Mesh.java 2014-11-23 22:35:24 UTC
(rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/shape/Mesh.java 2014-11-23 22:45:58 UTC
(rev 20120)
@@ -270,7 +270,7 @@
public boolean recalcAltVertices;
public short[] symopColixes;
-
+
protected void sumVertexNormals(T3[] vertices, V3[] normals) {
sumVertexNormals2(vertices, normals);
}
@@ -515,7 +515,7 @@
* @return unitcell
*/
public SymmetryInterface getUnitCell(Viewer vwr) {
- // isosurface only
+ // isosurfaceMesh only
return null;
}
Modified: branches/v14_2/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/shapesurface/Isosurface.java
2014-11-23 22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/shapesurface/Isosurface.java
2014-11-23 22:45:58 UTC (rev 20120)
@@ -487,6 +487,12 @@
return;
}
+ if ("processLattice" == propertyName) {
+ if (thisMesh != null)
+ thisMesh.processLattice(vwr);
+ return;
+ }
+
// Isosurface / SurfaceGenerator both interested
if ("slab" == propertyName) {
@@ -1409,9 +1415,16 @@
thisMesh.calculatedVolume = null;
// from JVXL file:
Parameters params = sg.getParams();
- if (!thisMesh.isMerged)
+ 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);
+ }
+ return;
+
+ }
if (!params.allowVolumeRender)
thisMesh.jvxlData.allowVolumeRender = false;
thisMesh.setColorsFromJvxlData(sg.getParams().colorRgb);
Modified: branches/v14_2/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
2014-11-23 22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
2014-11-23 22:45:58 UTC (rev 20120)
@@ -46,6 +46,7 @@
import javajs.util.M4;
import javajs.util.Measure;
import javajs.util.P3;
+import javajs.util.P3i;
import javajs.util.P4;
import javajs.util.PT;
import javajs.util.T3;
@@ -913,10 +914,63 @@
@Override
public SymmetryInterface getUnitCell(Viewer vwr) {
- return (spanningVectors == null ? null :
- Interface.getSymmetry(vwr, "symmetry").getUnitCell(spanningVectors, true,
null));
+ return (unitCell != null
+ || (unitCell = vwr.ms.am[modelIndex].biosymmetry) != null
+ || (unitCell = vwr.getModelUnitCell(modelIndex)) != null
+ || spanningVectors != null
+ && (unitCell = Interface.getSymmetry(vwr, "symmetry").getUnitCell(
+ spanningVectors, true, null)) != null ? unitCell : null);
}
+ void processLattice(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;
+ lattice = null;
+ unitCell.setMinMaxLatticeParameters(minXYZ, maxXYZ);
+ int nCells = (maxXYZ.x - minXYZ.x) * (maxXYZ.y - minXYZ.y)
+ * (maxXYZ.z - minXYZ.z);
+ P3 latticeOffset = new P3();
+ int vc0 = vc;
+ int vcNew = nCells * vc;
+ vs = AU.arrayCopyPt(vs, vcNew);
+ vvs = (vvs == null ? null : AU.ensureLengthA(vvs, vcNew));
+ int pc0 = pc;
+ int pcNew = nCells * pc;
+ pis = AU.arrayCopyII(pis, pcNew);
+ int off = 0;
+ normixes = AU.arrayCopyShort(normixes, vcNew);
+ for (int tx = minXYZ.x; tx < maxXYZ.x; tx++)
+ for (int ty = minXYZ.y; ty < maxXYZ.y; ty++)
+ for (int tz = minXYZ.z; tz < maxXYZ.z; tz++) {
+ if (tx == 0 && ty == 0 && tz == 0)
+ continue;
+ latticeOffset.set(tx, ty, tz);
+ unitCell.toCartesian(latticeOffset, false);
+ for (int i = 0; i < vc0; i++) {
+ normixes[vc] = normixes[i];
+ P3 v = P3.newP(vs[i]);
+ v.add(latticeOffset);
+ addVCVal(v, vvs[i], false);
+ }
+ off += vc0;
+ for (int i = 0; i < pc0; i++) {
+ int[] p = AU.arrayCopyI(pis[i], -1);
+ p[0] += off;
+ p[1] += off;
+ p[2] += off;
+ addPolygonC(p, 0, null);
+ }
+ }
+ P3 xyzMin = new P3();
+ P3 xyzMax = new P3();
+ setBox(xyzMin, xyzMax);
+ jvxlData.boundingBox = new P3[] { xyzMin, xyzMax };
+
+ }
+
/**
* "slabs" an isosurface into the first Brillouin zone moving points as
* necessary.
Modified: branches/v14_2/Jmol/src/org/jmol/util/BoxInfo.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/util/BoxInfo.java 2014-11-23 22:35:24 UTC
(rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/util/BoxInfo.java 2014-11-23 22:45:58 UTC
(rev 20120)
@@ -281,7 +281,7 @@
addPoint(pt, bbCorner0, bbCorner1, margin);
}
- public static void addPoint(T3 pt, P3 xyzMin, P3 xyzMax, float margin) {
+ public static void addPoint(T3 pt, T3 xyzMin, T3 xyzMax, float margin) {
if (pt.x - margin < xyzMin.x)
xyzMin.x = pt.x - margin;
if (pt.x + margin > xyzMax.x)
Modified: branches/v14_2/Jmol/src/org/jmol/util/MeshSurface.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/util/MeshSurface.java 2014-11-23
22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/util/MeshSurface.java 2014-11-23
22:45:58 UTC (rev 20120)
@@ -519,7 +519,6 @@
vertexSets[vc] = set;
}
int i = addVCVal(vertex, value, true);
- //int i = addVertexCopy(vertex, value, -4, true);
mapEdge.put(key, Integer.valueOf(i));
return i;
}
@@ -1090,4 +1089,14 @@
return newMesh(true, vectors, 0, faces, vectors, 0);
}
+ public void setBox(P3 xyzMin, P3 xyzMax) {
+ xyzMin.set(Float.MAX_VALUE, Float.MAX_VALUE, Float.MAX_VALUE);
+ xyzMax.set(-Float.MAX_VALUE, -Float.MAX_VALUE, -Float.MAX_VALUE);
+ for (int i = 0; i < vc; i++) {
+ T3 p = vs[i];
+ if (!Float.isNaN(p.x))
+ BoxInfo.addPoint(p, xyzMin, xyzMax, 0);
+ }
+ }
+
}
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-23
22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-23
22:45:58 UTC (rev 20120)
@@ -1,12 +1,14 @@
Jmol.___JmolDate="$Date$"
Jmol.___fullJmolProperties="src/org/jmol/viewer/Jmol.properties"
-
# THIS IS THE RELEASE BRANCH
# BUG FIXES ONLY, PLEASE
-Jmol.___JmolVersion="14.2.9_2014.11.21"
+Jmol.___JmolVersion="14.2.9_2014.11.23"
+released as Jmol 14.3.9 and Jmol 14.2.9
+
+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
@@ -168,7 +170,6 @@
bug fix: Legendre for D,U in Jana2006 reader not implemented - preliminary
JmolVersion="14.3.7_2014.10.13"
-released as Jmol 14.3.7
new feature: modulation occupancy settable using {*}.occupancy =
{*}.modulation('O',t)
-- for example:
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/OutputManager.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/OutputManager.java 2014-11-23
22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/OutputManager.java 2014-11-23
22:45:58 UTC (rev 20120)
@@ -107,7 +107,7 @@
/**
*
* Creates an image of params.type form -- PNG, PNGJ, PNGT, JPG, JPG64, PDF,
- * PPM, GIF, GIFT
+ * PPM, GIF, GIFT.
*
* From createImage and getImageAsBytes
*
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/StatusManager.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/StatusManager.java 2014-11-23
22:35:24 UTC (rev 20119)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/StatusManager.java 2014-11-23
22:45:58 UTC (rev 20120)
@@ -275,6 +275,7 @@
String callbackFunction) {
// menu and language setting also use this route
CBK callback = CBK.getCallback(callbackType);
+ System.out.println("callback set for " + callbackType + " " +
callbackFunction + " " + callback);
if (callback != null) {
int pt = (callbackFunction == null ? 0
: callbackFunction.length() > 7
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