--- trunk/src/applications/staticProps/GofXyz.cpp	2005/04/15 22:04:00	507
+++ trunk/src/applications/staticProps/GofXyz.cpp	2013/06/16 15:15:42	1879
@@ -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.
@@ -37,6 +28,16 @@
  * 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, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 
 #include <algorithm>
@@ -44,9 +45,11 @@
 #include "applications/staticProps/GofXyz.hpp"
 #include "utils/simError.h"
 #include "primitives/Molecule.hpp"
-namespace oopse {
+#include "types/MultipoleAdapter.hpp"
 
-  GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, double len, int nrbins)
+namespace OpenMD {
+
+  GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType len, int nrbins)
     : RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
       setOutputName(getPrefix(filename) + ".gxyz");
 
@@ -78,7 +81,7 @@ namespace oopse {
   }
 
 
-  void GofXyz::initalizeHistogram() {
+  void GofXyz::initializeHistogram() {
     //calculate the center of mass of the molecule of selected stuntdouble in selection1
 
     if (!evaluator3_.isDynamic()) {
@@ -100,14 +103,24 @@ namespace oopse {
     StuntDouble* sd3;
     
     for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j); 
-	 sd1 != NULL, sd3 != NULL;
+	 sd1 != NULL || sd3 != NULL;
 	 sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
 
-      Vector3d r3 =sd3->getPos();
+      Vector3d r3 = sd3->getPos();
       Vector3d r1 = sd1->getPos();
       Vector3d v1 =  r3 - r1;
-      info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
-      Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
+      if (usePeriodicBoundaryConditions_)
+        info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
+
+      AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
+      MultipoleAdapter ma1 = MultipoleAdapter(atype1);
+
+      Vector3d zaxis;
+      if (ma1.isDipole()) 
+        zaxis = sd1->getDipole();
+      else
+        zaxis = sd1->getA().transpose() * V3Z;
+
       Vector3d xaxis = cross(v1, zaxis);
       Vector3d yaxis = cross(zaxis, xaxis);
 
@@ -130,16 +143,17 @@ namespace oopse {
     Vector3d pos1 = sd1->getPos();
     Vector3d pos2 = sd2->getPos();
     Vector3d r12 = pos2 - pos1;
-    currentSnapshot_->wrapVector(r12);
+    if (usePeriodicBoundaryConditions_)
+      currentSnapshot_->wrapVector(r12);
 
     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_;
+    int xbin = int( (newR12.x() + halfLen_) / deltaR_);
+    int ybin = int( (newR12.y() + halfLen_) / deltaR_);
+    int zbin = int( (newR12.z() + halfLen_) / deltaR_);
 
     if (xbin < nRBins_ && xbin >=0 &&
         ybin < nRBins_ && ybin >= 0 &&
@@ -156,12 +170,11 @@ namespace oopse {
       //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) {
- 
-	for(int j = 0; j < histogram_[i].size(); ++j) {
- 
-	  for(int k = 0;k < histogram_[i][j].size(); ++k) {
-	    rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
+      for (unsigned int i = 0; i < histogram_.size(); ++i) { 
+	for(unsigned int j = 0; j < histogram_[i].size(); ++j) { 
+	  for(unsigned int k = 0;k < histogram_[i][j].size(); ++k) {
+	    rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ),
+                            sizeof(histogram_[i][j][k] ));
 	  }
 	}
       }