[Jmol-commits] SF.net SVN: jmol:[11698] trunk/Jmol/src/org/jmol/adapter/smarter/ AtomSetCollectionReader.java

[<ha...@us...>]

Revision: 11698
          http://jmol.svn.sourceforge.net/jmol/?rev=11698&view=rev
Author:   hansonr
Date:     2009-11-07 15:25:55 +0000 (Sat, 07 Nov 2009)

Log Message:
-----------
version=11.9.8_dev

# bug fix: GAMESS reader not reading all vibrational frequencies
# code: refactoring of readers to standardize vibration loading
#
# new feature: load "xxxx.xxx" [-vibration number]
#  loads only the specific vibration model.
#

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java

Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java	2009-11-07 15:25:11 UTC (rev 11697)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java	2009-11-07 15:25:55 UTC (rev 11698)
@@ -710,15 +710,10 @@
                                    boolean[] ignore, boolean isWide,
                                    int col0, int colWidth)
                                                      throws Exception {
-    String[][] data = new String[isWide ? atomCount : atomCount * 3][];
-    fillDataBlock(data, col0, colWidth);
-    fillFrequencies(data, iAtom0, atomCount, ignore, isWide);
-  }
-
-  protected void fillFrequencies(String[][] data, int iAtom0, int atomCount,
-                               boolean[] ignore, boolean isWide) {
+    int nLines = (isWide ? atomCount : atomCount * 3);
     int nFreq = ignore.length;
-    int nLines = data.length;
+    String[][] data = new String[nLines][];
+    fillDataBlock(data, col0, colWidth);
     for (int i = 0, atomPt = 0; i < nLines; i++, atomPt++) {
       String[] values = data[i];
       String[] valuesY = (isWide ? null : data[++i]);
@@ -731,6 +726,8 @@
         if (ignore[j])
           continue;
         int iAtom = iAtom0 + atomCount * j + atomPt;
+        if (Logger.debugging)
+          Logger.debug("vib " + iAtom + "/" + j + ": " + vx + " " + vy + " " + vz);
         atomSetCollection.addVibrationVector(iAtom, vx, vy, vz);
       }
     }


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