[Jmol-commits] CVS: Jmol/src/org/openscience/jmol CrystalFile.java,1.16.2.2,1.16.2.3 CrystalFrame.java,1.11.2.1,1.11.2.2

[Egon W. <eg...@us...>]

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol
In directory sc8-pr-cvs1:/tmp/cvs-serv13700/src/org/openscience/jmol

Modified Files:
      Tag: b6
	CrystalFile.java CrystalFrame.java 
Log Message:
Backported patch by Fabian to HEAD: 'Fixed problem reading some abinit files' and 'Fixed bug occuring while computing the BoundingBox when the unit frame collapse'

Index: CrystalFile.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/CrystalFile.java,v
retrieving revision 1.16.2.2
retrieving revision 1.16.2.3
diff -u -r1.16.2.2 -r1.16.2.3
--- CrystalFile.java	15 May 2003 13:25:32 -0000	1.16.2.2
+++ CrystalFile.java	14 Jun 2003 19:06:50 -0000	1.16.2.3
@@ -98,6 +98,49 @@
   // atomic position (double[3]) of each atom
 
 
+  //Compute the Unit Cell Box edges
+  static Vector boxEdgesTemplate = new Vector(24);
+  static {
+    boxEdgesTemplate.addElement(new Point3d());           //O
+    boxEdgesTemplate.addElement(new Point3d(1, 0, 0));    //E
+    
+    boxEdgesTemplate.addElement(new Point3d());           //O
+    boxEdgesTemplate.addElement(new Point3d(0, 1, 0));    //E
+    
+    boxEdgesTemplate.addElement(new Point3d());           //O
+    boxEdgesTemplate.addElement(new Point3d(0, 0, 1));    //E
+    
+    
+    boxEdgesTemplate.addElement(new Point3d(1, 0, 0));    //O
+    boxEdgesTemplate.addElement(new Point3d(1, 1, 0));    //E
+    
+    boxEdgesTemplate.addElement(new Point3d(1, 1, 0));    //O
+    boxEdgesTemplate.addElement(new Point3d(0, 1, 0));    //E
+    
+    boxEdgesTemplate.addElement(new Point3d(0, 1, 0));    //O
+    boxEdgesTemplate.addElement(new Point3d(0, 1, 1));    //E
+    
+    boxEdgesTemplate.addElement(new Point3d(0, 1, 1));    //O
+    boxEdgesTemplate.addElement(new Point3d(0, 0, 1));    //E
+    
+    boxEdgesTemplate.addElement(new Point3d(0, 0, 1));    //O
+    boxEdgesTemplate.addElement(new Point3d(1, 0, 1));    //E
+    
+    boxEdgesTemplate.addElement(new Point3d(1, 0, 1));    //O
+    boxEdgesTemplate.addElement(new Point3d(1, 0, 0));    //E
+    
+    boxEdgesTemplate.addElement(new Point3d(1, 0, 1));    //O
+    boxEdgesTemplate.addElement(new Point3d(1, 1, 1));    //E
+    
+    boxEdgesTemplate.addElement(new Point3d(1, 1, 1));    //O
+    boxEdgesTemplate.addElement(new Point3d(1, 1, 0));    //E
+    
+    boxEdgesTemplate.addElement(new Point3d(0, 1, 1));    //O
+    boxEdgesTemplate.addElement(new Point3d(1, 1, 1));    //E
+  }
+  
+
+
   /**
    * Default constructor:<br>
    * Create a CrystalFile object using default parameters.<br>
@@ -393,48 +436,11 @@
     double[][] unitBox = crystalBoxS.getUnitBox();
     int mina, minb, minc, maxa, maxb, maxc;
     Matrix3d op = new Matrix3d();
-    Vector boxEdgesTemplate = new Vector(24);
     Vector boxEdges = new Vector(1);
     Point3d vec;
     double[][] rprimd = unitCellBoxS.getRprimd();
 
-    //Compute the Unit Cell Box edges
-    boxEdgesTemplate.addElement(new Point3d());           //O
-    boxEdgesTemplate.addElement(new Point3d(1, 0, 0));    //E
 
-    boxEdgesTemplate.addElement(new Point3d());           //O
-    boxEdgesTemplate.addElement(new Point3d(0, 1, 0));    //E
-
-    boxEdgesTemplate.addElement(new Point3d());           //O
-    boxEdgesTemplate.addElement(new Point3d(0, 0, 1));    //E
-
-
-    boxEdgesTemplate.addElement(new Point3d(1, 0, 0));    //O
-    boxEdgesTemplate.addElement(new Point3d(1, 1, 0));    //E
-
-    boxEdgesTemplate.addElement(new Point3d(1, 1, 0));    //O
-    boxEdgesTemplate.addElement(new Point3d(0, 1, 0));    //E
-
-    boxEdgesTemplate.addElement(new Point3d(0, 1, 0));    //O
-    boxEdgesTemplate.addElement(new Point3d(0, 1, 1));    //E
-
-    boxEdgesTemplate.addElement(new Point3d(0, 1, 1));    //O
-    boxEdgesTemplate.addElement(new Point3d(0, 0, 1));    //E
-
-    boxEdgesTemplate.addElement(new Point3d(0, 0, 1));    //O
-    boxEdgesTemplate.addElement(new Point3d(1, 0, 1));    //E
-
-    boxEdgesTemplate.addElement(new Point3d(1, 0, 1));    //O
-    boxEdgesTemplate.addElement(new Point3d(1, 0, 0));    //E
-
-    boxEdgesTemplate.addElement(new Point3d(1, 0, 1));    //O
-    boxEdgesTemplate.addElement(new Point3d(1, 1, 1));    //E
-
-    boxEdgesTemplate.addElement(new Point3d(1, 1, 1));    //O
-    boxEdgesTemplate.addElement(new Point3d(1, 1, 0));    //E
-
-    boxEdgesTemplate.addElement(new Point3d(0, 1, 1));    //O
-    boxEdgesTemplate.addElement(new Point3d(1, 1, 1));    //E
 
     //Operator "op" needed to transform atomic crystal 
     //coordinate (atomCrystCoord) in cartesian atomic 
@@ -467,9 +473,37 @@
       }        //end j
     }          //end i
 
-    return boxEdges;
 
+    return boxEdges;
+    
+    
   }    //end generate UnitBoxFrame
+
+  /*
+   * Return the frame bounds corresponding to a single unit cell.
+   * This method is used by CrystalFrame.calcBoundingBox() when
+   * the boxEdges are 0 (no unit cell frame)
+   */
+  static public Vector getSingleBoxEdge(double[][] rprimd) {
+    Matrix3d op = new Matrix3d();
+    //Operator "op" needed to transform atomic crystal 
+    //coordinate (atomCrystCoord) in cartesian atomic 
+    //position (atomPos) 
+    op.transpose(MathUtil.arrayToMatrix3d(rprimd));
+
+    double[] redEdge = new double[3];
+    double[] cartEdge;
+    Vector boxEdgesDummy = new Vector(1);
+    for (int l = 0; l < boxEdgesTemplate.size(); l++) {  
+      redEdge[0] = ((Point3d) boxEdgesTemplate.elementAt(l)).x; 
+      redEdge[1] = ((Point3d) boxEdgesTemplate.elementAt(l)).y; 
+      redEdge[2] = ((Point3d) boxEdgesTemplate.elementAt(l)).z;
+      cartEdge = MathUtil.mulVec(op, redEdge);
+      boxEdgesDummy.addElement(new Point3d(cartEdge[0], cartEdge[1],
+					   cartEdge[2]));
+    }    //end l;
+    return boxEdgesDummy;
+  }
 
 
 

Index: CrystalFrame.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/CrystalFrame.java,v
retrieving revision 1.11.2.1
retrieving revision 1.11.2.2
diff -u -r1.11.2.1 -r1.11.2.2
--- CrystalFrame.java	15 May 2003 13:25:32 -0000	1.11.2.1
+++ CrystalFrame.java	14 Jun 2003 19:06:51 -0000	1.11.2.2
@@ -66,11 +66,19 @@
   }
 
   void calcBoundingBox() {
+
+    Vector boxEdges;
+    if (this.boxEdges.isEmpty()) {
+      boxEdges = CrystalFile.getSingleBoxEdge(rprimd);
+    } else {
+      boxEdges = this.boxEdges;
+    }
+    
     Point3d position = (Point3d) boxEdges.elementAt(0);
     double minX = position.x, maxX = minX;
     double minY = position.y, maxY = minY;
     double minZ = position.z, maxZ = minZ;
-
+    
     for (int i = 1, size = boxEdges.size(); i < size; ++i) {
       position = (Point3d) boxEdges.elementAt(i);
       double x = position.x;
@@ -84,12 +92,12 @@
       if (z > maxZ) { maxZ = z; }
     }
     centerBoundingBox = new Point3d((minX + maxX) / 2,
-                                    (minY + maxY) / 2,
-                                    (minZ + maxZ) / 2);
+				    (minY + maxY) / 2,
+				    (minZ + maxZ) / 2);
     cornerBoundingBox = new Point3d(maxX, maxY, maxZ);
     cornerBoundingBox.sub(centerBoundingBox);
   }
-
+  
   // arrowhead size isn't included because it is currently in screen
   // coordinates .. oh well. 
   public double calcRadius(Point3d center) {