Revision: 20133
http://sourceforge.net/p/jmol/code/20133
Author: hansonr
Date: 2014-11-26 04:04:14 +0000 (Wed, 26 Nov 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.10_2014.11.27"
new feature: isosurface LATTICE + x.x ....
-- for periodic lattices only
-- expands one unit cell by x.x in fractional coordinates
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/Parameters.java
trunk/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
trunk/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
2014-11-25 18:53:34 UTC (rev 20132)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
2014-11-26 04:04:14 UTC (rev 20133)
@@ -95,6 +95,14 @@
@Override
protected void getPeriodicVoxels() throws Exception {
+ rd();
+ String[] tokens = getTokens();
+ if (nSkip > 0 && tokens.length < 3 + nSurfaces) {
+ for (int j = 0; j < nSkip; j++)
+ for (int i = 0; i < nFilePoints; i++)
+ rd();
+ nSkip = 0;
+ }
int dsf = downsampleFactor;
if (dsf > 1) {
for (int i = 0; i < nFilePoints; i++) {
@@ -119,7 +127,6 @@
rd();
}
}
-
}
private void skipPoints(int n) {
@@ -135,18 +142,5 @@
next[0] = pt;
}
-
- @Override
- protected void readSkip() throws Exception {
- rd();
- String[] tokens = getTokens();
- if (nSkip > 0 && tokens.length < 3 + nSurfaces) {
- for (int j = 0; j < nSkip; j++)
- for (int i = 0; i < nFilePoints; i++)
- rd();
- nSkip = 0;
- }
- }
-
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/Parameters.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/Parameters.java 2014-11-25
18:53:34 UTC (rev 20132)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/Parameters.java 2014-11-26
04:04:14 UTC (rev 20133)
@@ -226,6 +226,7 @@
distance = Float.MAX_VALUE;
doFullMolecular = false;
envelopeRadius = 10f;
+ extendLattice = 0;
fileIndex = 1;
readAllData = true;
fileName = "";
@@ -246,9 +247,9 @@
isMapped = false;
isPeriodic = false;
isSilent = false;
- mapLattice = null;
logCube = logCompression = false;
logMessages = Logger.debugging;
+ mapLattice = null;
mappedDataMin = Float.MAX_VALUE;
mep_calcType = -1;
minSet = 0;
@@ -821,6 +822,7 @@
public VolumeData volumeData;
public ContactPair contactPair;
public P3 mapLattice;
+ public float extendLattice;
public boolean isMapped;
public boolean showTiming;
public float pointSize;
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
2014-11-25 18:53:34 UTC (rev 20132)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
2014-11-26 04:04:14 UTC (rev 20133)
@@ -6,25 +6,51 @@
protected void readSurfaceData(boolean isMapData) throws Exception {
initializeSurfaceData();
voxelData = new float[nPointsX][nPointsY][nPointsZ];
- readSkip();
getPeriodicVoxels();
+ if (params.extendLattice > 0) {
+ float f = params.extendLattice;
+ int[] n = new int[3];
+ int nx = nPointsX - 1;
+ int ny = nPointsY - 1;
+ int nz = nPointsZ - 1;
+ for (int i = 0; i < 3; i++) {
+ int vi = voxelCounts[i] - 1;
+ n[i] = (int) (vi * f);
+ volumetricOrigin.scaleAdd2(-n[i], volumetricVectors[i],
+ volumetricOrigin);
+ vi += 2 * n[i];
+ while (n[i] > 0)
+ n[i] -= voxelCounts[i] - 1;
+ voxelCounts[i] = vi + 1;
+ }
+ nPointsX = voxelCounts[0];
+ nPointsY = voxelCounts[1];
+ nPointsZ = voxelCounts[2];
+ float[][][] vd = new float[nPointsX][nPointsY][nPointsZ];
+ for (int i = nPointsX; --i >= 0;)
+ for (int j = nPointsY; --j >= 0;)
+ for (int k = nPointsZ; --k >= 0;) {
+ vd[i][j][k] = voxelData[(i - n[0]) % nx][(j - n[1]) % ny][(k -
n[2]) % nz];
+ }
+ voxelData = vd;
+ } else {
- // add in periodic face data
+ // add in periodic face data
- int n;
- n = nPointsX - 1;
- for (int i = 0; i < nPointsY; ++i)
- for (int j = 0; j < nPointsZ; ++j)
- voxelData[n][i][j] = voxelData[0][i][j];
- n = nPointsY - 1;
- for (int i = 0; i < nPointsX; ++i)
- for (int j = 0; j < nPointsZ; ++j)
- voxelData[i][n][j] = voxelData[i][0][j];
- n = nPointsZ - 1;
- for (int i = 0; i < nPointsX; ++i)
- for (int j = 0; j < nPointsY; ++j)
- voxelData[i][j][n] = voxelData[i][j][0];
-
+ int n;
+ n = nPointsX - 1;
+ for (int i = 0; i < nPointsY; ++i)
+ for (int j = 0; j < nPointsZ; ++j)
+ voxelData[n][i][j] = voxelData[0][i][j];
+ n = nPointsY - 1;
+ for (int i = 0; i < nPointsX; ++i)
+ for (int j = 0; j < nPointsZ; ++j)
+ voxelData[i][n][j] = voxelData[i][0][j];
+ n = nPointsZ - 1;
+ for (int i = 0; i < nPointsX; ++i)
+ for (int j = 0; j < nPointsY; ++j)
+ voxelData[i][j][n] = voxelData[i][j][0];
+ }
// for map data, just pick out near points and get rid of voxelData
if (isMapData && volumeData.hasPlane()) {
@@ -41,12 +67,14 @@
voxelData = null;
}
volumeData.setVoxelDataAsArray(voxelData);
-
+
if (dataMin > params.cutoff)
params.cutoff = 2 * dataMin;
}
protected abstract void getPeriodicVoxels() throws Exception;
- protected abstract void readSkip() throws Exception;
+ static {
+ System.out.println(-5 % 10);
+ }
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java 2014-11-25
18:53:34 UTC (rev 20132)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java 2014-11-26
04:04:14 UTC (rev 20133)
@@ -803,6 +803,11 @@
return true;
}
+ if ("extendLattice" == propertyName) {
+ params.extendLattice = ((Float) value).floatValue();
+ return true;
+ }
+
// / final actions ///
if ("property" == propertyName) {
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java 2014-11-25
18:53:34 UTC (rev 20132)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java 2014-11-26
04:04:14 UTC (rev 20133)
@@ -137,13 +137,6 @@
}
}
-
- @Override
- protected void readSkip() throws Exception {
- // n/a
- }
-
-
}
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-11-25 18:53:34 UTC
(rev 20132)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-11-26 04:04:14 UTC
(rev 20133)
@@ -4153,7 +4153,8 @@
sigma = 3;
addShapeProperty(propertyList, "sign", Boolean.TRUE);
}
- showString("using cutoff = " + cutoff + (Float.isNaN(sigma) ? ""
: " sigma=" + sigma));
+ showString("using cutoff = " + cutoff
+ + (Float.isNaN(sigma) ? "" : " sigma=" + sigma));
if (!Float.isNaN(sigma)) {
cutoff *= sigma;
sigma = Float.NaN;
@@ -4271,23 +4272,30 @@
case T.lattice:
if (iShape != JC.SHAPE_ISOSURFACE)
invArg();
- pt = getPoint3f(eval.iToken + 1, false);
- i = eval.iToken;
- if (pt.x <= 0 || pt.y <= 0 || pt.z <= 0)
- break;
- pt.x = (int) pt.x;
- pt.y = (int) pt.y;
- pt.z = (int) pt.z;
- sbCommand.append(" lattice ").append(Escape.eP(pt));
- if (isMapped) {
- propertyName = "mapLattice";
- propertyValue = pt;
+ if (tokAt(i + 1) == T.plus) {
+ i += 2;
+ propertyName = "extendLattice";
+ propertyValue = Float.valueOf(floatParameter(i));
+ sbCommand.append(" lattice + " + propertyValue);
} else {
- lattice = pt;
- if (tokAt(i + 1) == T.on) {
- sbCommand.append(" true");
- processLattice = true;
- i++;
+ pt = getPoint3f(i + 1, false);
+ i = eval.iToken;
+ if (pt.x <= 0 || pt.y <= 0 || pt.z <= 0)
+ break;
+ pt.x = (int) pt.x;
+ pt.y = (int) pt.y;
+ pt.z = (int) pt.z;
+ sbCommand.append(" lattice ").append(Escape.eP(pt));
+ if (isMapped) {
+ propertyName = "mapLattice";
+ propertyValue = pt;
+ } else {
+ lattice = pt;
+ if (tokAt(i + 1) == T.on) {
+ sbCommand.append(" true");
+ processLattice = true;
+ i++;
+ }
}
}
break;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-25 18:53:34 UTC
(rev 20132)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-26 04:04:14 UTC
(rev 20133)
@@ -15,8 +15,14 @@
TODO: design and implement sidechain mutation -- MUTATE command ?
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.10_2014.11.26"
+Jmol.___JmolVersion="14.3.10_2014.11.27"
+new feature: isosurface LATTICE + x.x ....
+ -- for periodic lattices only
+ -- expands one unit cell by x.x in fractional coordinates
+
+JmolVersion="14.3.10_2014.11.26"
+
bug fix: hover OFF disables hover callback, but should not
bug fix: reading of JVXL file saved with noFill still does fill
bug fix: CASTEP DENSITY surface file reader does not do downsampling
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