Changes in src/Actions/AnalysisAction/PairCorrelationAction.cpp [623e89:112b09]

File:

• src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) (4 diffs)

src/Actions/AnalysisAction/PairCorrelationAction.cpp

@@ -6 +6 @@
  */
 
+#include "Helpers/MemDebug.hpp"
+
 #include "Actions/AnalysisAction/PairCorrelationAction.hpp"
+#include "CommandLineParser.hpp"
 #include "analysis_correlation.hpp"
-#include "boundary.hpp"
-#include "linkedcell.hpp"
 #include "log.hpp"
 #include "element.hpp"
-#include "molecule.hpp"
 #include "periodentafel.hpp"
-#include "vector.hpp"
 #include "World.hpp"
 
@@ -38 +37 @@
   Dialog *dialog = UIFactory::getInstance().makeDialog();
   int ranges[3] = {1, 1, 1};
+  double BinStart = 0.;
   double BinEnd = 0.;
-  double BinStart = 0.;
-  double BinWidth = 0.;
-  molecule *Boundary = NULL;
   string outputname;
   string binoutputname;
@@ -47 +44 @@
   ofstream output;
   ofstream binoutput;
-  std::vector< element *> elements;
-  string type;
-  Vector Point;
-  BinPairMap *binmap = NULL;
-  MoleculeListClass *molecules = World::getInstance().getMolecules();
+  const element *elemental1;
+  const element *elemental2;
 
-  // first dialog: Obtain which type of correlation
-  dialog->queryString(NAME, &type, MapOfActions::getInstance().getDescription(NAME));
-  if(dialog->display()) {
-    delete dialog;
-  } else {
-    delete dialog;
-    return Action::failure;
-  }
-
-  // second dialog: Obtain parameters specific to this type
-  dialog = UIFactory::getInstance().makeDialog();
-  if (type == "P")
-    dialog->queryVector("position", &Point, World::getInstance().getDomain(), false, MapOfActions::getInstance().getDescription("position"));
-  if (type == "S")
-    dialog->queryMolecule("molecule-by-id", &Boundary, MapOfActions::getInstance().getDescription("molecule-by-id"));
-  dialog->queryElement("elements", &elements, MapOfActions::getInstance().getDescription("elements"));
+  dialog->queryElement("elements", &elemental1, MapOfActions::getInstance().getDescription("elements"));
+  dialog->queryElement("elements", &elemental2, MapOfActions::getInstance().getDescription("elements"));
   dialog->queryDouble("bin-start", &BinStart, MapOfActions::getInstance().getDescription("bin-start"));
-  dialog->queryDouble("bin-width", &BinWidth, MapOfActions::getInstance().getDescription("bin-width"));
   dialog->queryDouble("bin-end", &BinEnd, MapOfActions::getInstance().getDescription("bin-end"));
   dialog->queryString("output-file", &outputname, MapOfActions::getInstance().getDescription("output-file"));
@@ -80 +59 @@
     binoutput.open(binoutputname.c_str());
     PairCorrelationMap *correlationmap = NULL;
-    if (type == "E") {
-      PairCorrelationMap *correlationmap = NULL;
-      if (periodic)
-        correlationmap = PeriodicPairCorrelation(World::getInstance().getMolecules(), elements, ranges);
-      else
-        correlationmap = PairCorrelation(World::getInstance().getMolecules(), elements);
-      //OutputCorrelationToSurface(&output, correlationmap);
-      binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
-    } else if (type == "P")  {
-      cout << "Point to correlate to is  " << Point << endl;
-      CorrelationToPointMap *correlationmap = NULL;
-      if (periodic)
-        correlationmap  = PeriodicCorrelationToPoint(molecules, elements, &Point, ranges);
-      else
-        correlationmap = CorrelationToPoint(molecules, elements, &Point);
-      //OutputCorrelationToSurface(&output, correlationmap);
-      binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
-    } else if (type == "S") {
-      ASSERT(Boundary != NULL, "No molecule specified for SurfaceCorrelation.");
-      const double radius = 4.;
-      double LCWidth = 20.;
-      if (BinEnd > 0) {
-        if (BinEnd > 2.*radius)
-            LCWidth = BinEnd;
-        else
-          LCWidth = 2.*radius;
-      }
-
-      // get the boundary
-      class Tesselation *TesselStruct = NULL;
-      const LinkedCell *LCList = NULL;
-      // find biggest molecule
-      int counter  = molecules->ListOfMolecules.size();
-      bool *Actives = new bool[counter];
-      counter = 0;
-      for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
-        Actives[counter++] = (*BigFinder)->ActiveFlag;
-        (*BigFinder)->ActiveFlag = (*BigFinder == Boundary) ? false : true;
-      }
-      LCList = new LinkedCell(Boundary, LCWidth);
-      FindNonConvexBorder(Boundary, TesselStruct, LCList, radius, NULL);
-      CorrelationToSurfaceMap *surfacemap = NULL;
-      if (periodic)
-        surfacemap = PeriodicCorrelationToSurface( molecules, elements, TesselStruct, LCList, ranges);
-      else
-        surfacemap = CorrelationToSurface( molecules, elements, TesselStruct, LCList);
-      OutputCorrelationToSurface(&output, surfacemap);
-      // check whether radius was appropriate
-      {
-        double start; double end;
-        GetMinMax( surfacemap, start, end);
-        if (LCWidth < end)
-          DoeLog(1) && (eLog()<< Verbose(1) << "Linked Cell width is smaller than the found range of values! Bins can only be correct up to: " << radius << "." << endl);
-      }
-      binmap = BinData( surfacemap, BinWidth, BinStart, BinEnd );
-    } else
-      return Action::failure;
+    if (periodic)
+      correlationmap = PeriodicPairCorrelation(World::getInstance().getMolecules(), elemental1, elemental2, ranges);
+    else
+      correlationmap = PairCorrelation(World::getInstance().getMolecules(), elemental1, elemental2);
+    //OutputCorrelationToSurface(&output, correlationmap);
+    BinPairMap *binmap = BinData( correlationmap, 0.5, BinStart, BinEnd );
     OutputCorrelation ( &binoutput, binmap );
     output.close();