--- trunk/src/applications/staticProps/GofR.cpp	2005/02/09 17:08:22	306
+++ trunk/src/applications/staticProps/GofR.cpp	2012/08/22 18:43:27	1785
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,81 +28,106 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
+ * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 
 #include <algorithm>
 #include <fstream>
 #include "applications/staticProps/GofR.hpp"
+#include "utils/simError.h"
 
-namespace oopse {
+namespace OpenMD {
 
-GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len)
-    : RadialDistrFunc(info, filename, sele1, sele2, len){
+  GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins)
+    : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){
 
-    histogram_.resize(nbins_);
-    avgGofr_.resize(nbins_);
-}
+      deltaR_ = len_ /nRBins_;
+    
+      histogram_.resize(nRBins_);
+      avgGofr_.resize(nRBins_);
 
+      setOutputName(getPrefix(filename) + ".gofr");
+    }
 
-void GofR::preProcess() {
-    avgGofr_.resize(nbins_);
+
+  void GofR::preProcess() {
     std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0);    
-}
+  }
 
-void GofR::initalizeHistogram() {
-    npairs_ = 0;
+  void GofR::initializeHistogram() {
     std::fill(histogram_.begin(), histogram_.end(), 0);
-}
+  }
 
 
-void GofR::processHistogram() {
+  void GofR::processHistogram() {
 
-    double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
-    double pairDensity = npairs_ /volume;
-    double pairConstant = ( 4.0 * PI * pairDensity ) / 3.0;
+    int nPairs = getNPairs();
+    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
+    RealType pairDensity = nPairs /volume * 2.0;
+    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
 
-    for(int i = 0 ; i < histogram_.size(); ++i){
+    for(unsigned int i = 0 ; i < histogram_.size(); ++i){
 
-        double rLower = i * delta_;
-        double rUpper = rLower + delta_;
-        double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
-        double nIdeal = volSlice * pairConstant;
+      RealType rLower = i * deltaR_;
+      RealType rUpper = rLower + deltaR_;
+      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
+      RealType nIdeal = volSlice * pairConstant;
 
-        avgGofr_[i] += histogram_[i] / nIdeal;    
+      avgGofr_[i] += histogram_[i] / nIdeal;    
     }
 
-}
+  }
 
-void GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
+  void GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
 
     if (sd1 == sd2) {
-        return;
+      return;
     }
     
     Vector3d pos1 = sd1->getPos();
     Vector3d pos2 = sd2->getPos();
-    Vector3d r12 = pos1 - pos2;
-    
-    double distance = (pos1 - pos2).length();
+    Vector3d r12 = pos2 - pos1;
+    if (usePeriodicBoundaryConditions_)
+      currentSnapshot_->wrapVector(r12);
 
-    int whichBin = distance / delta_;
-    histogram_[whichBin] ++;
-    npairs_++;
-}
+    RealType distance = r12.length();
 
+    if (distance < len_) {
+      int whichBin = distance / deltaR_;
+      histogram_[whichBin] += 2;
+    }
+  }
 
-void GofR::writeRdf() {
+
+  void GofR::writeRdf() {
     std::ofstream rdfStream(outputFilename_.c_str());
     if (rdfStream.is_open()) {
-        rdfStream << "#radial distribution function\n";
-        rdfStream << "#selection1: " << selectionScript1_;
-        rdfStream << "#selection2: " << selectionScript2_;
-        
+      rdfStream << "#radial distribution function\n";
+      rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
+      rdfStream << "selection2: (" << selectionScript2_ << ")\n";
+      rdfStream << "#r\tcorrValue\n";
+      for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
+	RealType r = deltaR_ * (i + 0.5);
+	rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n";
+      }
     } else {
 
-
+      sprintf(painCave.errMsg, "GofR: unable to open %s\n", outputFilename_.c_str());
+      painCave.isFatal = 1;
+      simError();  
     }
-}
 
+    rdfStream.close();
+  }
+
 }