Changes in src/analysis_correlation.cpp [c78d44:58bbd3]

File:

• src/analysis_correlation.cpp (modified) (3 diffs)

src/analysis_correlation.cpp

@@ -179 +179 @@
   }
 
-//  outmap = new PairCorrelationMap;
-//  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
-//    if ((*MolWalker)->ActiveFlag) {
-//      double * FullMatrix = ReturnFullMatrixforSymmetric(World::getInstance().getDomain());
-//      double * FullInverseMatrix = InverseMatrix(FullMatrix);
-//      DoeLog(2) && (eLog()<< Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
-//      for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
-//        DoLog(3) && (Log() << Verbose(3) << "Current atom is " << **iter << "." << endl);
-//        if ((type1 == NULL) || ((*iter)->type == type1)) {
-//          periodicX = *(*iter)->node;
-//          periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
-//          // go through every range in xyz and get distance
-//          for (n[0]=-ranges[0]; n[0] <= ranges[0]; n[0]++)
-//            for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
-//              for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
-//                checkX = Vector(n[0], n[1], n[2]) + periodicX;
-//                checkX.MatrixMultiplication(FullMatrix);
-//                for (MoleculeList::const_iterator MolOtherWalker = MolWalker; MolOtherWalker != molecules->ListOfMolecules.end(); MolOtherWalker++)
-//                  if ((*MolOtherWalker)->ActiveFlag) {
-//                    DoLog(2) && (Log() << Verbose(2) << "Current other molecule is " << *MolOtherWalker << "." << endl);
-//                    for (molecule::const_iterator runner = (*MolOtherWalker)->begin(); runner != (*MolOtherWalker)->end(); ++runner) {
-//                      DoLog(3) && (Log() << Verbose(3) << "Current otheratom is " << **runner << "." << endl);
-//                      if ((*iter)->nr < (*runner)->nr)
-//                        if ((type2 == NULL) || ((*runner)->type == type2)) {
-//                          periodicOtherX = *(*runner)->node;
-//                          periodicOtherX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
-//                          // go through every range in xyz and get distance
-//                          for (Othern[0]=-ranges[0]; Othern[0] <= ranges[0]; Othern[0]++)
-//                            for (Othern[1]=-ranges[1]; Othern[1] <= ranges[1]; Othern[1]++)
-//                              for (Othern[2]=-ranges[2]; Othern[2] <= ranges[2]; Othern[2]++) {
-//                                checkOtherX = Vector(Othern[0], Othern[1], Othern[2]) + periodicOtherX;
-//                                checkOtherX.MatrixMultiplication(FullMatrix);
-//                                distance = checkX.distance(checkOtherX);
-//                                //Log() << Verbose(1) <<"Inserting " << *(*iter) << " and " << *(*runner) << endl;
-//                                outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> ((*iter), (*runner)) ) );
-//                              }
-//                        }
-//                  }
-//              }
-//            }
-//        }
-//      }
-//      delete[](FullMatrix);
-//      delete[](FullInverseMatrix);
-//    }
-
   return outmap;
 };
@@ -239 +193 @@
   CorrelationToPointMap *outmap = NULL;
   double distance = 0.;
+  double *cell_size = World::getInstance().getDomain();
 
   if (molecules->ListOfMolecules.empty()) {
@@ -254 +209 @@
         for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
           if ((*type == NULL) || ((*iter)->type == *type)) {
-            distance = (*iter)->node->PeriodicDistance(*point, World::getInstance().getDomain());
+            distance = (*iter)->node->PeriodicDistance(*point, cell_size);
             DoLog(4) && (Log() << Verbose(4) << "Current distance is " << distance << "." << endl);
             outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> ((*iter), point) ) );