[Jmol-commits] SF.net SVN: jmol: [5222] branches/bob200603/Jmol/src/org/jmol/viewer

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

Revision: 5222
Author:   hansonr
Date:     2006-06-13 20:19:21 -0700 (Tue, 13 Jun 2006)
ViewCVS:  http://svn.sourceforge.net/jmol/?rev=5222&view=rev

Log Message:
-----------
bob200603 isosurface adds anisotropy

Modified Paths:
--------------
    branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java
    branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java	2006-06-14 02:25:31 UTC (rev 5221)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java	2006-06-14 03:19:21 UTC (rev 5222)
@@ -4021,21 +4021,21 @@
         switch (statement[++i].tok) {
         case Token.dollarsign:
           String id = objectNameParameter(++i);
-            propertyValue = viewer.getDrawObjectCenter(id);
-            if (propertyValue == null)
-              drawObjectNotDefined(id);
+          propertyValue = viewer.getDrawObjectCenter(id);
+          if (propertyValue == null)
+            drawObjectNotDefined(id);
           break;
         case Token.expressionBegin:
-            propertyValue = viewer.getAtomSetCenter(expression(statement, i + 1));
-            i = pcLastExpressionInstruction;
+          propertyValue = viewer.getAtomSetCenter(expression(statement, i + 1));
+          i = pcLastExpressionInstruction;
           break;
         case Token.leftbrace:
-            propertyValue = getCoordinate(i, true);
-            i = pcLastExpressionInstruction;
-            break;
+          propertyValue = getCoordinate(i, true);
+          i = pcLastExpressionInstruction;
+          break;
         default:
           coordinateOrNameOrExpressionRequired();
-          }
+        }
         break;
       case Token.leftbrace:
         // {X, Y, Z, W}
@@ -4062,6 +4062,12 @@
         break;
       case Token.identifier:
         String str = (String) token.value;
+        if (str.equalsIgnoreCase("ANISOTROPY")) {
+          propertyName = "anisotropy";
+          propertyValue = getCoordinate(i + 1, false);
+          i = pcLastExpressionInstruction;
+          break;
+        }
         if (str.equalsIgnoreCase("FIXED")) {
           propertyName = "fixed";
           propertyValue = Boolean.TRUE;
@@ -4072,7 +4078,7 @@
           propertyValue = Boolean.FALSE;
           break;
         }
-        
+
         if (str.equalsIgnoreCase("sign")) {
           signPt = i + 1;
           propertyName = "sign";
@@ -4116,9 +4122,9 @@
           nlmZR[0] = intParameter(++i);
           nlmZR[1] = intParameter(++i);
           nlmZR[2] = intParameter(++i);
-          nlmZR[3] = (statement[i + 1].tok == Token.integer ? floatParameter(++i)
+          nlmZR[3] = (statement.length > i + 1 && statement[i + 1].tok == Token.integer ? floatParameter(++i)
               : 6f);
-          nlmZR[4] = (statement[i + 1].tok == Token.integer ? floatParameter(++i)
+          nlmZR[4] = (statement.length > i + 1 && statement[i + 1].tok == Token.integer ? floatParameter(++i)
               : 10f);
           propertyName = "orbital";
           propertyValue = nlmZR;

Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java	2006-06-14 02:25:31 UTC (rev 5221)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java	2006-06-14 03:19:21 UTC (rev 5222)
@@ -120,6 +120,8 @@
   boolean isOrbital;
   boolean isSolvent;
   boolean isFunctionXY;
+  float[] anisotropy = new float[3];
+
   float solventRadius;
 
   int edgeFractionBase;
@@ -163,7 +165,7 @@
   int nContours;
   int thisContour;
   boolean dotsOnly;
-  boolean isFixed; 
+  boolean isFixed;
 
   BufferedReader br;
 
@@ -197,11 +199,20 @@
       isFunctionXY = false;
       isCalculation = false;
       center.set(Float.MAX_VALUE, Float.MAX_VALUE, Float.MAX_VALUE);
+      anisotropy[0]  = anisotropy[1] = anisotropy[2] = 1f;
       cutoff = Float.MAX_VALUE;
       super.setProperty("meshID", null, null);
       return;
     }
 
+    if ("anisotropy" == propertyName) {
+      Point3f pt = (Point3f) value;
+      anisotropy[0] = pt.x;
+      anisotropy[1] = pt.y;
+      anisotropy[2] = pt.z;
+      return;
+    }
+
     if ("center" == propertyName) {
       center.set((Point3f) value);
       return;
@@ -715,7 +726,7 @@
     isJvxlColorMapped = false;
     isJvxlColorPrecision = false;
     thisInside = (!isJvxl || thePlane == null);
-    if(insideOut) 
+    if (insideOut)
       thisInside = !thisInside;
     nDataPoints = 0;
     voxelData = new float[nPointsX][][];
@@ -2834,9 +2845,9 @@
     ptXyz.scaleAdd((voxelCounts[0] - 1) / 2f, volumetricVectors[0], ptXyz);
     ptXyz.scaleAdd((voxelCounts[1] - 1) / 2f, volumetricVectors[1], ptXyz);
     ptXyz.scaleAdd((voxelCounts[2] - 1) / 2f, volumetricVectors[2], ptXyz);
-    System.out.println("teset1 "+volumetricOrigin);
+    System.out.println("teset1 " + volumetricOrigin);
     volumetricOrigin.sub(center, ptXyz);
-    System.out.println("teset2 "+volumetricOrigin);
+    System.out.println("teset2 " + volumetricOrigin);
   }
 
   Point3f pixelPtToXYZ(int x, int y) {
@@ -2961,16 +2972,17 @@
   void setupOrbital() {
     psi_radiusAngstroms = autoScaleOrbital();
     if (center.x == Float.MAX_VALUE)
-      psiOrigin.set(0,0,0);
+      psiOrigin.set(0, 0, 0);
     else
       psiOrigin.set(center);
     for (int i = 0; i < 3; i++)
-      setVoxelRange(i, -psi_radiusAngstroms, psi_radiusAngstroms,
-          psi_ptsPerAngstrom, psi_gridMax);
+      setVoxelRange(i, -psi_radiusAngstroms * anisotropy[i],
+          psi_radiusAngstroms * anisotropy[i], psi_ptsPerAngstrom, psi_gridMax);
 
     jvxlFileHeader = "orbital psi squared\nn=" + psi_n + ", l=" + psi_l
         + ", m=" + psi_m + " Znuc=" + psi_Znuc + " res=" + psi_ptsPerAngstrom
-        + " rad=" + psi_radiusAngstroms + "\n";
+        + " rad=" + psi_radiusAngstroms + " anisotropy=(" + anisotropy[0] + ","
+        + anisotropy[1] + "," + anisotropy[2] + ")\n";
 
     jvxlFileHeader += jvxlGetVolumeHeader();
     atomCount = 0;
@@ -3017,9 +3029,9 @@
   double hydrogenAtomPsiAt(Point3f pt, int n, int el, int m) {
     // ref: http://www.stolaf.edu/people/hansonr/imt/concept/schroed.pdf
     int abm = Math.abs(m);
-    float x = pt.x - psiOrigin.x;
-    float y = pt.y - psiOrigin.y;
-    float z = pt.z - psiOrigin.z;
+    float x = (pt.x - psiOrigin.x) / anisotropy[0];
+    float y = (pt.y - psiOrigin.y) / anisotropy[1];
+    float z = (pt.z - psiOrigin.z) / anisotropy[2];
     double x2y2 = x * x + y * y;
     double r2 = x2y2 + z * z;
     double r = Math.sqrt(r2);
@@ -3263,7 +3275,7 @@
       System.out.println(x + " " + y + " " + zValue + " " + (z - zValue));
     return z - zValue;
   }
-  
+
   void setModelIndex() {
     if (currentMesh == null)
       return;
@@ -3275,9 +3287,9 @@
       currentMesh.modelIndex = -1;
     } else {
       currentMesh.modelIndex = viewer.getDisplayModelIndex();
-    }  
+    }
   }
-  
+
   void setVisibilityFlags(BitSet bs) {
     /*
      * set all fixed objects visible; others based on model being displayed
@@ -3285,10 +3297,10 @@
      */
     for (int i = meshCount; --i >= 0;) {
       Mesh mesh = meshes[i];
-      mesh.visibilityFlags = 
-        (mesh.visible && (mesh.modelIndex < 0 || bs.get(mesh.modelIndex)) ? myVisibilityFlag : 0);
+      mesh.visibilityFlags = (mesh.visible
+          && (mesh.modelIndex < 0 || bs.get(mesh.modelIndex)) ? myVisibilityFlag
+          : 0);
     }
   }
 
-
 }


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