[Jmol-commits] SF.net SVN: jmol: [5518] branches/v10_9/Jmol/src/org/jmol/adapter/smarter/ AtomSetCollection.java

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

Revision: 5518
          http://svn.sourceforge.net/jmol/?rev=5518&view=rev
Author:   hansonr
Date:     2006-09-13 11:48:59 -0700 (Wed, 13 Sep 2006)

Log Message:
-----------
bug fix checking for duplicate atoms in applySymmetry()

Modified Paths:
--------------
    branches/v10_9/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java

Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java	2006-09-13 18:17:06 UTC (rev 5517)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java	2006-09-13 18:48:59 UTC (rev 5518)
@@ -385,11 +385,13 @@
     SymmetryOperation[] finalOperations = spaceGroup.getFinalOperations(atoms, atomIndex, count);
     for (int i = 0; i < count; i++)
       atoms[i + atomIndex].bsSymmetry = new BitSet();
+    int operationCount = finalOperations.length;
+    cartesians = new Point3f[count * operationCount * maxX * maxY * maxZ];
+    int pt = 0;
     for (int tx = 0; tx < maxX; tx++)
       for (int ty = 0; ty < maxY; ty++)
         for (int tz = 0; tz < maxZ; tz++)
-          symmetryAddAtoms(finalOperations, atomIndex, count, tx, ty, tz);
-    int operationCount = finalOperations.length;
+          pt = symmetryAddAtoms(finalOperations, atomIndex, count, tx, ty, tz, pt);
     if (operationCount > 0) {
       String[] symmetryList = new String[operationCount];
       for (int i = 0; i < operationCount; i++)
@@ -407,20 +409,20 @@
   }
   
   Point3f[] cartesians;
-  void symmetryAddAtoms(SymmetryOperation[] finalOperations, int atomIndex,
-                        int count, int transX, int transY, int transZ) {
+  int symmetryAddAtoms(SymmetryOperation[] finalOperations, int atomIndex,
+                        int count, int transX, int transY, int transZ, int pt) {
     boolean isBaseCell = (transX == 0 && transY == 0 && transZ == 0);
     int nOperations = finalOperations.length;
-    cartesians = new Point3f[count * nOperations];
-    int pt = 0;
     if (isBaseCell)
+      pt = 0;
       for (; pt < count; pt++) {
         Atom atom = atoms[atomIndex + pt];
         cartesians[pt] = new Point3f(atom);
         finalOperations[0].transform(cartesians[pt]);
         atom.bsSymmetry.set(0);
       }
-    for (int iSym = 0; iSym < nOperations; iSym++)
+    for (int iSym = 0; iSym < nOperations; iSym++) {
+      int pt0 = pt;
       if (!isBaseCell || !finalOperations[iSym].getXyz().equals("x,y,z")) {
         int i1 = atomIndex;
         int i2 = i1 + count;
@@ -430,40 +432,44 @@
               .newPoint(atoms[i], atom, transX, transY, transZ);
           Point3f cartesian = new Point3f(atom);
           unitCell.toCartesian(cartesian);
+
           /*
-           System.out.println((Point3f) atoms[i] + " " + (Point3f) atom + " "
-           + transX + " " + transY + " " + transZ + " " + cartesian
-           + finalOperations[iSym].getXyz());
-           */
+          System.out.println((Point3f) atoms[i] + " " + (Point3f) atom + " "
+              + transX + " " + transY + " " + transZ + " " + cartesian
+              + finalOperations[iSym].getXyz());
+          */
+  
           Atom special = null;
-          for (int j = pt; --j >= 0;)
+          for (int j = pt0; --j >= 0;) {
+//            System.out.println(j + ": " + cartesians[j] + " ?cart? " + cartesian + " d=" + cartesian.distance(cartesians[j]));
+
             if (cartesian.distance(cartesians[j]) < 0.01) {
               special = atoms[atomIndex + j];
               break;
             }
-          if (special != null) {
+          }
+          if (special == null) {
+            Atom atom1 = newCloneAtom(atoms[i]);
+            atom1.x = atom.x;
+            atom1.y = atom.y;
+            atom1.z = atom.z;
+  //          System.out.println(cartesian + " " + (Point3f)atom + "X" + finalOperations[iSym].getXyz() + " " + transX+" "+transY+" "+transZ);
+            atom1.atomSite = atoms[i].atomSite;
+            atom1.bsSymmetry = new BitSet();
+            atom1.bsSymmetry.set(iSym);
+            cartesians[pt++] = cartesian;
+          } else {
             special.bsSymmetry.set(iSym);
             /*
              System.out.println(iSym + " " + finalOperations[iSym].getXyz()
              + " special set: " + i + " " + " " + special.bsSymmetry);
              */
-            continue;
+    //        System.out.println(cartesian+"Y" + "X" + finalOperations[iSym].getXyz() + " " + transX+" "+transY+" "+transZ);
           }
-          Atom atom1 = newCloneAtom(atoms[i]);
-          atom1.x = atom.x;
-          atom1.y = atom.y;
-          atom1.z = atom.z;
-          atom1.atomSite = atoms[i].atomSite;
-          atom1.bsSymmetry = new BitSet();
-          atom1.bsSymmetry.set(iSym);
-          cartesians[pt++] = cartesian;
-          /*
-           System.out.println(iSym + " " + finalOperations[iSym].getXyz()
-           + " setting: " + i + " " + " " + atom.atomName + " "
-           + atom1.atomName + " " + atom1.bsSymmetry);
-           */
         }
       }
+    }
+    return pt;
   }
   
   void setCollectionName(String collectionName) {


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