[Jmol-commits] SF.net SVN: jmol:[10810] trunk/Jmol/src/org/jmol/adapter/readers/more

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

Revision: 10810
          http://jmol.svn.sourceforge.net/jmol/?rev=10810&view=rev
Author:   hansonr
Date:     2009-04-16 14:21:33 +0000 (Thu, 16 Apr 2009)

Log Message:
-----------
version=11.7.33_dev # new feature: load xxxx FILTER "NBOcharges" loads NBO charges instead of Mulliken
#   note: for NBOs you still need FILTER "NBO" so with charges that would be FILTER "NBO;NBOcharges"

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/adapter/readers/more/GaussianReader.java
    trunk/Jmol/src/org/jmol/adapter/readers/more/MOReader.java

Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/GaussianReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/GaussianReader.java	2009-04-15 18:58:57 UTC (rev 10809)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/GaussianReader.java	2009-04-16 14:21:33 UTC (rev 10810)
@@ -593,6 +593,7 @@
   void readPartialCharges() throws Exception {
     discardLines(1);
     int atomCount = atomSetCollection.getAtomCount();
+    int firstAtomCount = atomSetCollection.getFirstAtomSetAtomCount();
     int i0 = atomSetCollection.getLastAtomSetAtomIndex();
     Atom[] atoms = atomSetCollection.getAtoms();
     for (int i = i0; i < atomCount; ++i) {
@@ -600,8 +601,8 @@
       while (atoms[i].elementNumber == 0)
         ++i;
       // assign the partial charge
-      atoms[i].partialCharge =
-        parseFloat(getTokens(readLine())[2]);
+      float charge = parseFloat(getTokens(readLine())[2]);
+      atoms[i].partialCharge = (haveNboCharges ? atoms[i0 % firstAtomCount].partialCharge : charge);
     }
   }
   

Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/MOReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/MOReader.java	2009-04-15 18:58:57 UTC (rev 10809)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/MOReader.java	2009-04-16 14:21:33 UTC (rev 10810)
@@ -89,6 +89,7 @@
   protected Vector moTypes;
   private boolean getNBOs;
   private boolean getNBOCharges;
+  protected boolean haveNboCharges;
 
   private String[] filterTokens;
   private boolean filterIsNot; 
@@ -200,10 +201,14 @@
  ===============================================================================
 
    */
+  
   private void getNboCharges() throws Exception {
+    if (haveNboCharges)
+      return; // don't use alpha/beta spin charges
     discardLinesUntilContains("----");
     discardLinesUntilContains("----");
     int atomCount = atomSetCollection.getFirstAtomSetAtomCount();
+    haveNboCharges = true;
     for (int i = 0; i < atomCount; i++) {
       String[] tokens = getTokens(readLine());
       float charge;


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