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[Jmol-commits] SF.net SVN: jmol:[11696] branches/v11_8/Jmol/src/org
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From: <ha...@us...> - 2009-11-07 13:32:23
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Revision: 11696
http://jmol.svn.sourceforge.net/jmol/?rev=11696&view=rev
Author: hansonr
Date: 2009-11-07 13:32:10 +0000 (Sat, 07 Nov 2009)
Log Message:
-----------
version=11.8.9_dev # bug fix: GAMESS reader not reading all vibrational frequencies
Modified Paths:
--------------
branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GamessReader.java
branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v11_8/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
Modified: branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GamessReader.java
===================================================================
--- branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GamessReader.java 2009-11-07 12:13:04 UTC (rev 11695)
+++ branches/v11_8/Jmol/src/org/jmol/adapter/readers/more/GamessReader.java 2009-11-07 13:32:10 UTC (rev 11696)
@@ -139,26 +139,26 @@
// now contains all atoms across all models (optimization steps).
// We only want to set vetor data corresponding to new cloned
// models and not interfere with the previous ones.
- float[] xComponents = new float[5];
- float[] yComponents = new float[5];
- float[] zComponents = new float[5];
- float[] frequencies = new float[5];
+ float[] xComponents = new float[10];
+ float[] yComponents = new float[10];
+ float[] zComponents = new float[10];
+ float[] frequencies = new float[10];
discardLinesUntilContains("FREQUENCY:");
while (line != null && line.indexOf("FREQUENCY:") >= 0) {
- int lineFreqCount = 0;
+ int frequencyCount = 0;
String[] tokens = getTokens();
for (int i = 0; i < tokens.length; i++) {
float frequency = parseFloat(tokens[i]);
if (tokens[i].equals("I"))
- frequencies[lineFreqCount - 1] = -frequencies[lineFreqCount - 1];
+ frequencies[frequencyCount - 1] = -frequencies[frequencyCount - 1];
if (Float.isNaN(frequency))
continue; // may be "I" for imaginary
- frequencies[lineFreqCount] = frequency;
- lineFreqCount++;
+ frequencies[frequencyCount] = frequency;
+ frequencyCount++;
if (Logger.debugging) {
Logger.debug(totalFrequencyCount + " frequency=" + frequency);
}
- if (lineFreqCount == 5)
+ if (frequencyCount == frequencies.length)
break;
}
String[] red_masses = null;
@@ -171,7 +171,7 @@
if (line.indexOf("INTENS") >= 0) {
intensities = getTokens();
}
- for (int i = 0; i < lineFreqCount; i++) {
+ for (int i = 0; i < frequencyCount; i++) {
++totalFrequencyCount;
// The last model should be cloned because we might
// have done an optimization with HSSEND=.TRUE.
@@ -181,11 +181,12 @@
atomSetCollection.setAtomSetProperty("Frequency", frequencies[i]
+ " cm-1");
if (red_masses != null)
- atomSetCollection.setAtomSetProperty("Reduced Mass", red_masses[i + 2]
- + " AMU");
+ atomSetCollection.setAtomSetProperty("Reduced Mass",
+ red_masses[red_masses.length - frequencyCount + i] + " AMU");
if (intensities != null)
- atomSetCollection.setAtomSetProperty("IR Intensity", intensities[i + 2]
- + " D^2/AMU-Angstrom^2");
+ atomSetCollection.setAtomSetProperty("IR Intensity",
+ intensities[intensities.length - frequencyCount + i]
+ + " D^2/AMU-Angstrom^2");
}
Atom[] atoms = atomSetCollection.getAtoms();
@@ -196,15 +197,15 @@
for (int i = 0; i < atomCount; ++i) {
atomIndex = index0 + i;
readLine();
- readComponents(lineFreqCount, xComponents);
+ readComponents(frequencyCount, xComponents);
readLine();
- readComponents(lineFreqCount, yComponents);
+ readComponents(frequencyCount, yComponents);
readLine();
- readComponents(lineFreqCount, zComponents);
+ readComponents(frequencyCount, zComponents);
//This loop applies the normal mode displacements
//to atom i across all clones (frequencies) by finding
//its position in atoms[].
- for (int j = 0; j < lineFreqCount; ++j) {
+ for (int j = 0; j < frequencyCount; ++j) {
atomIndex += atomCount;
Atom atom = atoms[atomIndex];
atom.vectorX = xComponents[j];
Modified: branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-07 12:13:04 UTC (rev 11695)
+++ branches/v11_8/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-07 13:32:10 UTC (rev 11696)
@@ -4,6 +4,8 @@
version=11.8.9_dev
+# bug fix: GAMESS reader not reading all vibrational frequencies
+
# -----------------------------------------------------------------------------
#version=11.8.8
Modified: branches/v11_8/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
===================================================================
--- branches/v11_8/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java 2009-11-07 12:13:04 UTC (rev 11695)
+++ branches/v11_8/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java 2009-11-07 13:32:10 UTC (rev 11696)
@@ -1529,7 +1529,7 @@
*
*/
public float[][] functionXY(String functionName, int nX, int nY) {
- nX = Math.abs(nX);
+/* nX = Math.abs(nX);
nY = Math.abs(nY);
float[][] f = new float[nX][nY];
//boolean isSecond = (functionName.indexOf("2") >= 0);
@@ -1547,6 +1547,23 @@
}
return f; // for user-defined isosurface functions (testing only -- bob hanson)
+ */
+
+ nX = Math.abs(nX);
+ nY = Math.abs(nY);
+ float[][] f = new float[nX][nY];
+ boolean isSecond = (functionName.indexOf("2") >= 0);
+
+ for (int i = nX; --i >= 0;)
+ for (int j = nY; --j >= 0;) {
+ f[i][j] = (isSecond ? (float) ((i + j - nX) / (2f)) : (float) Math
+ .sqrt(Math.abs(i * i + j * j)) / 2f);
+ //if (i < 10 && j < 10)
+ //System.out.println(" functionXY " + i + " " + j + " " + f[i][j]);
+ }
+
+ return f; // for user-defined isosurface functions (testing only -- bob hanson)
+
}
public float[][][] functionXYZ(String functionName, int nX, int nY, int nZ) {
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