--- trunk/src/applications/staticProps/GofXyz.cpp	2005/02/10 22:37:21	311
+++ trunk/src/applications/staticProps/GofXyz.cpp	2005/03/28 15:54:04	448
@@ -43,108 +43,137 @@
 #include <fstream>
 #include "applications/staticProps/GofXyz.hpp"
 #include "utils/simError.h"
-
+#include "primitives/Molecule.hpp"
 namespace oopse {
 
-GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
-    : RadialDistrFunc(info, filename, sele1, sele2){
+GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, double len, int nrbins)
+    : RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
     setOutputName(getPrefix(filename) + ".gxyz");
 
+    evaluator3_.loadScriptString(sele3);
+    if (!evaluator3_.isDynamic()) {
+        seleMan3_.setSelectionSet(evaluator3_.evaluate());
+    }    
+
+    deltaR_ =  len_ / nRBins_;
+    
+    histogram_.resize(nRBins_);
+    for (int i = 0 ; i < nRBins_; ++i) {
+        histogram_[i].resize(nRBins_);
+        for(int j = 0; j < nRBins_; ++j) {
+            histogram_[i][j].resize(nRBins_);
+        }
+    }   
+   
 }
 
 
 void GofXyz::preProcess() {
-    /*
-    for (int i = 0; i < avgGofr_.size(); ++i) {
-        std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
-    }
-    */
+    for (int i = 0 ; i < nRBins_; ++i) {
+        histogram_[i].resize(nRBins_);
+        for(int j = 0; j < nRBins_; ++j) {
+            std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
+        }
+    }   
 }
 
+
 void GofXyz::initalizeHistogram() {
-    /*
-    npairs_ = 0;
-    for (int i = 0; i < histogram_.size(); ++i)
-        std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
-    */
-}
+    //calculate the center of mass of the molecule of selected stuntdouble in selection1
 
+    if (!evaluator3_.isDynamic()) {
+        seleMan3_.setSelectionSet(evaluator3_.evaluate());
+    }    
 
-void GofXyz::processHistogram() {
+    assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
+    
+    //dipole direction of selection3 and position of selection3 will be used to determine the y-z plane
+    //v1 = s3 -s1, 
+    //z = origin.dipole
+    //x = v1 X z
+    //y = z X x 
+    rotMats_.clear();
 
-    /*
-    double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
-    double pairDensity = npairs_ /volume;
-    double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
+    int i;
+    int j;
+    StuntDouble* sd1;
+    StuntDouble* sd3;
+    
+    for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j); 
+        sd1 != NULL, sd3 != NULL;
+        sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
 
-    for(int i = 0 ; i < histogram_.size(); ++i){
+        Vector3d r3 =sd3->getPos();
+        Vector3d r1 = sd1->getPos();
+        Vector3d v1 =  r3 - r1;
+        info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
+        Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
+        Vector3d xaxis = cross(v1, zaxis);
+        Vector3d yaxis = cross(zaxis, xaxis);
 
-        double rLower = i * deltaR_;
-        double rUpper = rLower + deltaR_;
-        double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
-        double nIdeal = volSlice * pairConstant;
+        xaxis.normalize();
+        yaxis.normalize();
+        zaxis.normalize();
 
-        for (int j = 0; j < histogram_[i].size(); ++j){
-            avgGofr_[i][j] += histogram_[i][j] / nIdeal;    
-        }
+        RotMat3x3d rotMat;
+        rotMat.setRow(0, xaxis);
+        rotMat.setRow(1, yaxis);
+        rotMat.setRow(2, zaxis);
+        
+        rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
     }
-    */
+
 }
 
 void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
 
-    /*
-    if (sd1 == sd2) {
-        return;
-    }
-    
     Vector3d pos1 = sd1->getPos();
     Vector3d pos2 = sd2->getPos();
-    Vector3d r12 = pos1 - pos2;
+    Vector3d r12 = pos2 - pos1;
     currentSnapshot_->wrapVector(r12);
 
-    double distance = r12.length();
-    int whichRBin = distance / deltaR_;
+    std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
+    assert(i != rotMats_.end());
+    
+    Vector3d newR12 = i->second * r12;
+    // x, y and z's possible values range -halfLen_ to halfLen_
+    int xbin = (newR12.x()+ halfLen_) / deltaR_;
+    int ybin = (newR12.y() + halfLen_) / deltaR_;
+    int zbin = (newR12.z() + halfLen_) / deltaR_;
 
+    if (xbin < nRBins_ && xbin >=0 &&
+        ybin < nRBins_ && ybin >= 0 &&
+        zbin < nRBins_ && zbin >=0 ) {
+        ++histogram_[xbin][ybin][zbin];
+    }
     
-    double cosAngle = evaluateAngle(sd1, sd2);
-    double halfBin = (nAngleBins_ - 1) * 0.5;
-    int whichThetaBin = halfBin * (cosAngle + 1.0)
-    ++histogram_[whichRBin][whichThetaBin];
-    
-    ++npairs_;
-    */
 }
 
 void GofXyz::writeRdf() {
-    std::ofstream rdfStream(outputFilename_.c_str());
+    std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
     if (rdfStream.is_open()) {
-        rdfStream << "#radial distribution function\n";
-        rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
-        rdfStream << "selection2: (" << selectionScript2_ << ")\n";
-        rdfStream << "#r\tcorrValue\n";
+        //rdfStream << "#g(x, y, z)\n";
+        //rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
+        //rdfStream << "selection2: (" << selectionScript2_ << ")\n";
+        //rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
         for (int i = 0; i < histogram_.size(); ++i) {
-            double x = deltaR_ * (i + 0.5);
-
+ 
             for(int j = 0; j < histogram_[i].size(); ++j) {
-                double y = deltaR_ * (j+ 0.5);
-
-                for(int k = 0;k < histogram_[i].size(); ++k) {
-                    double z = deltaR_ * (k + 0.5); 
-                    rdfStream << x << "\t" << y << "\t" <<  z << "\t" << histogram_[i][j][k]/nProcessed_ << "\n";
+ 
+                for(int k = 0;k < histogram_[i][j].size(); ++k) {
+                    rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
                 }
             }
         }
         
     } else {
 
-
+        sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
+        painCave.isFatal = 1;
+        simError();  
     }
 
     rdfStream.close();
 }
 
 }
-
-
-