--- trunk/src/applications/staticProps/RadialDistrFunc.cpp	2005/02/10 22:37:21	311
+++ trunk/src/applications/staticProps/RadialDistrFunc.cpp	2005/02/16 19:36:30	353
@@ -48,7 +48,8 @@ RadialDistrFunc::        RadialDistrFunc(SimInfo* info
 
 RadialDistrFunc::        RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
         : info_(info), currentSnapshot_(NULL), dumpFilename_(filename), step_(1), 
-          selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){
+          selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), 
+          seleMan1_(info), seleMan2_(info), common_(info), sele1_minus_common_(info), sele2_minus_common_(info){
           
     evaluator1_.loadScriptString(sele1);
     evaluator2_.loadScriptString(sele2);
@@ -60,6 +61,19 @@ RadialDistrFunc::        RadialDistrFunc(SimInfo* info
             seleMan2_.setSelectionSet(evaluator2_.evaluate());
     }
 
+    if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) {
+        //if all selections are static,  we can precompute the number of real pairs    
+        common_ = seleMan1_ & seleMan2_;
+        sele1_minus_common_ = seleMan1_ - common_;
+        sele2_minus_common_ = seleMan2_ - common_;      
+
+        int nSelected1 = seleMan1_.getSelectionCount();
+        int nSelected2 = seleMan2_.getSelectionCount();
+        int nIntersect = common_.getSelectionCount();
+        
+        nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;            
+    }
+    
 }
 
 void RadialDistrFunc::process() {
@@ -67,11 +81,13 @@ void RadialDistrFunc::process() {
     RigidBody* rb;
     SimInfo::MoleculeIterator mi;
     Molecule::RigidBodyIterator rbIter;
+    
     preProcess();
     
     DumpReader reader(info_, dumpFilename_);    
     int nFrames = reader.getNFrames();
-    nProcessed_ = nFrames / step_ + 1;
+    nProcessed_ = nFrames / step_;
+
     for (int i = 0; i < nFrames; i += step_) {
         reader.readFrame(i);
         currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
@@ -93,17 +109,40 @@ void RadialDistrFunc::process() {
         
         initalizeHistogram();
 
-        StuntDouble* sd1;
-        int j;
-        for (sd1 = seleMan1_.beginSelected(j); sd1 != NULL; sd1 = seleMan1_.nextSelected(j)) {
 
-            StuntDouble* sd2;
-            int k;
-            for (sd2 = seleMan2_.beginSelected(k); sd2 != NULL; sd2 = seleMan2_.nextSelected(k)) {
-                collectHistogram(sd1, sd2);
-            }            
+        
+        //selections may overlap.
+        //
+        // |s1 -c | c |
+        //            | c |s2 - c|
+        //
+        // s1 : number of selected stuntdoubles in selection1
+        // s2 : number of selected stuntdoubles in selection2
+        // c   : number of intersect stuntdouble between selection1 and selection2
+        //when loop over the pairs, we can divide the looping into 3 stages
+        //stage 1 :     [s1-c]      [s2]
+        //stage 2 :     [c]            [s2 - c]
+        //stage 3 :     [c]            [c]
+        //stage 1 and stage 2 are completly non-overlapping
+        //stage 3 are completely overlapping
+
+        if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) {
+
+            common_ = seleMan1_ & seleMan2_;
+            sele1_minus_common_ = seleMan1_ - common_;
+            sele2_minus_common_ = seleMan2_ - common_;            
+            int nSelected1 = seleMan1_.getSelectionCount();
+            int nSelected2 = seleMan2_.getSelectionCount();
+            int nIntersect = common_.getSelectionCount();
+            
+            nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;                      
         }
 
+        processNonOverlapping(sele1_minus_common_, seleMan2_);
+        processNonOverlapping(common_, sele2_minus_common_);        
+        processOverlapping(common_);
+        
+        
         processHistogram();
         
     }
@@ -113,4 +152,37 @@ void RadialDistrFunc::process() {
     writeRdf();
 }
 
+void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, SelectionManager& sman2) {
+    StuntDouble* sd1;
+    StuntDouble* sd2;
+    int i;    
+    int j;
+    
+    for (sd1 = sman1.beginSelected(i); sd1 != NULL; sd1 = sman1.nextSelected(i)) {
+
+        for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) {
+            collectHistogram(sd1, sd2);
+        }            
+    }
+
 }
+
+void RadialDistrFunc::processOverlapping( SelectionManager& sman) {
+    StuntDouble* sd1;
+    StuntDouble* sd2;
+    int i;    
+    int j;
+
+    //basically, it is the same as below loop
+    //for (int i = 0;  i < n; ++i )
+    //  for (int j = i + 1; j < n; ++j) {}
+    
+    for (sd1 = sman.beginSelected(i); sd1 != NULL; sd1 = sman.nextSelected(i)) {                    
+        for (j  = i, sd2 = sman.nextSelected(j); sd2 != NULL; sd2 = sman.nextSelected(j)) {
+            collectHistogram(sd1, sd2);
+        }            
+    }
+
+}
+
+}