Changes in src/analysis_correlation.cpp [1614174:a67d19]

File:

• src/analysis_correlation.cpp (modified) (24 diffs)

src/analysis_correlation.cpp

@@ -10 +10 @@
 #include "analysis_correlation.hpp"
 #include "element.hpp"
+#include "info.hpp"
 #include "log.hpp"
 #include "molecule.hpp"
 #include "tesselation.hpp"
 #include "tesselationhelpers.hpp"
+#include "triangleintersectionlist.hpp"
 #include "vector.hpp"
 #include "verbose.hpp"
+#include "World.hpp"
 
 
@@ -28 +31 @@
 PairCorrelationMap *PairCorrelation(MoleculeListClass * const &molecules, const element * const type1, const element * const type2 )
 {
+  Info FunctionInfo(__func__);
   PairCorrelationMap *outmap = NULL;
   double distance = 0.;
 
   if (molecules->ListOfMolecules.empty()) {
-    eLog() << Verbose(1) <<"No molecule given." << endl;
+    DoeLog(1) && (eLog()<< Verbose(1) <<"No molecule given." << endl);
     return outmap;
   }
@@ -38 +42 @@
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     if ((*MolWalker)->ActiveFlag) {
-      eLog() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
-      atom *Walker = (*MolWalker)->start;
-      while (Walker->next != (*MolWalker)->end) {
-        Walker = Walker->next;
-        Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl;
+      DoeLog(2) && (eLog()<< Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
+      atom *Walker = (*MolWalker)->start;
+      while (Walker->next != (*MolWalker)->end) {
+        Walker = Walker->next;
+        DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
         if ((type1 == NULL) || (Walker->type == type1)) {
           for (MoleculeList::const_iterator MolOtherWalker = MolWalker; MolOtherWalker != molecules->ListOfMolecules.end(); MolOtherWalker++)
             if ((*MolOtherWalker)->ActiveFlag) {
-              Log() << Verbose(2) << "Current other molecule is " << *MolOtherWalker << "." << endl;
+              DoLog(2) && (Log() << Verbose(2) << "Current other molecule is " << *MolOtherWalker << "." << endl);
               atom *OtherWalker = (*MolOtherWalker)->start;
               while (OtherWalker->next != (*MolOtherWalker)->end) { // only go up to Walker
                 OtherWalker = OtherWalker->next;
-                Log() << Verbose(3) << "Current otheratom is " << *OtherWalker << "." << endl;
+                DoLog(3) && (Log() << Verbose(3) << "Current otheratom is " << *OtherWalker << "." << endl);
                 if (Walker->nr < OtherWalker->nr)
                   if ((type2 == NULL) || (OtherWalker->type == type2)) {
-                    distance = Walker->node->PeriodicDistance(OtherWalker->node, (*MolWalker)->cell_size);
+                    distance = Walker->node->PeriodicDistance(OtherWalker->node, World::get()->cell_size);
                     //Log() << Verbose(1) <<"Inserting " << *Walker << " and " << *OtherWalker << endl;
                     outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> (Walker, OtherWalker) ) );
@@ -77 +81 @@
 PairCorrelationMap *PeriodicPairCorrelation(MoleculeListClass * const &molecules, const element * const type1, const element * const type2, const int ranges[NDIM] )
 {
+  Info FunctionInfo(__func__);
   PairCorrelationMap *outmap = NULL;
   double distance = 0.;
@@ -87 +92 @@
 
   if (molecules->ListOfMolecules.empty()) {
-    eLog() << Verbose(1) <<"No molecule given." << endl;
+    DoeLog(1) && (eLog()<< Verbose(1) <<"No molecule given." << endl);
     return outmap;
   }
@@ -93 +98 @@
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     if ((*MolWalker)->ActiveFlag) {
-      double * FullMatrix = ReturnFullMatrixforSymmetric((*MolWalker)->cell_size);
+      double * FullMatrix = ReturnFullMatrixforSymmetric(World::get()->cell_size);
       double * FullInverseMatrix = InverseMatrix(FullMatrix);
-      eLog() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
-      atom *Walker = (*MolWalker)->start;
-      while (Walker->next != (*MolWalker)->end) {
-        Walker = Walker->next;
-        Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl;
+      DoeLog(2) && (eLog()<< Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
+      atom *Walker = (*MolWalker)->start;
+      while (Walker->next != (*MolWalker)->end) {
+        Walker = Walker->next;
+        DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
         if ((type1 == NULL) || (Walker->type == type1)) {
           periodicX.CopyVector(Walker->node);
@@ -112 +117 @@
                 for (MoleculeList::const_iterator MolOtherWalker = MolWalker; MolOtherWalker != molecules->ListOfMolecules.end(); MolOtherWalker++)
                   if ((*MolOtherWalker)->ActiveFlag) {
-                    Log() << Verbose(2) << "Current other molecule is " << *MolOtherWalker << "." << endl;
+                    DoLog(2) && (Log() << Verbose(2) << "Current other molecule is " << *MolOtherWalker << "." << endl);
                     atom *OtherWalker = (*MolOtherWalker)->start;
                     while (OtherWalker->next != (*MolOtherWalker)->end) { // only go up to Walker
                       OtherWalker = OtherWalker->next;
-                      Log() << Verbose(3) << "Current otheratom is " << *OtherWalker << "." << endl;
+                      DoLog(3) && (Log() << Verbose(3) << "Current otheratom is " << *OtherWalker << "." << endl);
                       if (Walker->nr < OtherWalker->nr)
                         if ((type2 == NULL) || (OtherWalker->type == type2)) {
@@ -154 +159 @@
 CorrelationToPointMap *CorrelationToPoint(MoleculeListClass * const &molecules, const element * const type, const Vector *point )
 {
+  Info FunctionInfo(__func__);
   CorrelationToPointMap *outmap = NULL;
   double distance = 0.;
 
   if (molecules->ListOfMolecules.empty()) {
-    Log() << Verbose(1) <<"No molecule given." << endl;
+    DoLog(1) && (Log() << Verbose(1) <<"No molecule given." << endl);
     return outmap;
   }
@@ -164 +170 @@
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     if ((*MolWalker)->ActiveFlag) {
-      Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
-      atom *Walker = (*MolWalker)->start;
-      while (Walker->next != (*MolWalker)->end) {
-        Walker = Walker->next;
-        Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl;
+      DoLog(2) && (Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
+      atom *Walker = (*MolWalker)->start;
+      while (Walker->next != (*MolWalker)->end) {
+        Walker = Walker->next;
+        DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
         if ((type == NULL) || (Walker->type == type)) {
-          distance = Walker->node->PeriodicDistance(point, (*MolWalker)->cell_size);
-          Log() << Verbose(4) << "Current distance is " << distance << "." << endl;
+          distance = Walker->node->PeriodicDistance(point, World::get()->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*> (Walker, point) ) );
         }
@@ -190 +196 @@
 CorrelationToPointMap *PeriodicCorrelationToPoint(MoleculeListClass * const &molecules, const element * const type, const Vector *point, const int ranges[NDIM] )
 {
+  Info FunctionInfo(__func__);
   CorrelationToPointMap *outmap = NULL;
   double distance = 0.;
@@ -197 +204 @@
 
   if (molecules->ListOfMolecules.empty()) {
-    Log() << Verbose(1) <<"No molecule given." << endl;
+    DoLog(1) && (Log() << Verbose(1) <<"No molecule given." << endl);
     return outmap;
   }
@@ -203 +210 @@
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     if ((*MolWalker)->ActiveFlag) {
-      double * FullMatrix = ReturnFullMatrixforSymmetric((*MolWalker)->cell_size);
+      double * FullMatrix = ReturnFullMatrixforSymmetric(World::get()->cell_size);
       double * FullInverseMatrix = InverseMatrix(FullMatrix);
-      Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
-      atom *Walker = (*MolWalker)->start;
-      while (Walker->next != (*MolWalker)->end) {
-        Walker = Walker->next;
-        Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl;
+      DoLog(2) && (Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
+      atom *Walker = (*MolWalker)->start;
+      while (Walker->next != (*MolWalker)->end) {
+        Walker = Walker->next;
+        DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
         if ((type == NULL) || (Walker->type == type)) {
           periodicX.CopyVector(Walker->node);
@@ -221 +228 @@
                 checkX.MatrixMultiplication(FullMatrix);
                 distance = checkX.Distance(point);
-                Log() << Verbose(4) << "Current distance is " << distance << "." << endl;
+                DoLog(4) && (Log() << Verbose(4) << "Current distance is " << distance << "." << endl);
                 outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> (Walker, point) ) );
               }
@@ -243 +250 @@
 CorrelationToSurfaceMap *CorrelationToSurface(MoleculeListClass * const &molecules, const element * const type, const Tesselation * const Surface, const LinkedCell *LC )
 {
+  Info FunctionInfo(__func__);
   CorrelationToSurfaceMap *outmap = NULL;
   double distance = 0;
@@ -249 +257 @@
 
   if ((Surface == NULL) || (LC == NULL) || (molecules->ListOfMolecules.empty())) {
-    Log() << Verbose(1) <<"No Tesselation, no LinkedCell or no molecule given." << endl;
+    DoeLog(1) && (eLog()<< Verbose(1) <<"No Tesselation, no LinkedCell or no molecule given." << endl);
     return outmap;
   }
@@ -255 +263 @@
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     if ((*MolWalker)->ActiveFlag) {
-      Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
-      atom *Walker = (*MolWalker)->start;
-      while (Walker->next != (*MolWalker)->end) {
-        Walker = Walker->next;
-        Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl;
+      DoLog(1) && (Log() << Verbose(1) << "Current molecule is " << (*MolWalker)->name << "." << endl);
+      atom *Walker = (*MolWalker)->start;
+      while (Walker->next != (*MolWalker)->end) {
+        Walker = Walker->next;
+        //Log() << Verbose(1) << "Current atom is " << *Walker << "." << endl;
         if ((type == NULL) || (Walker->type == type)) {
-          triangle = Surface->FindClosestTriangleToPoint(Walker->node, LC );
-          if (triangle != NULL) {
-            distance = DistanceToTrianglePlane(Walker->node, triangle);
-            outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> (Walker, triangle) ) );
-          }
-        }
-      }
-    }
+          TriangleIntersectionList Intersections(Walker->node,Surface,LC);
+          distance = Intersections.GetSmallestDistance();
+          triangle = Intersections.GetClosestTriangle();
+          outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> (Walker, triangle) ) );
+        }
+      }
+    } else
+      DoLog(1) && (Log() << Verbose(1) << "molecule " << (*MolWalker)->name << " is not active." << endl);
+
 
   return outmap;
@@ -288 +297 @@
 CorrelationToSurfaceMap *PeriodicCorrelationToSurface(MoleculeListClass * const &molecules, const element * const type, const Tesselation * const Surface, const LinkedCell *LC, const int ranges[NDIM] )
 {
+  Info FunctionInfo(__func__);
   CorrelationToSurfaceMap *outmap = NULL;
   double distance = 0;
@@ -297 +307 @@
 
   if ((Surface == NULL) || (LC == NULL) || (molecules->ListOfMolecules.empty())) {
-    Log() << Verbose(1) <<"No Tesselation, no LinkedCell or no molecule given." << endl;
+    DoLog(1) && (Log() << Verbose(1) <<"No Tesselation, no LinkedCell or no molecule given." << endl);
     return outmap;
   }
   outmap = new CorrelationToSurfaceMap;
-  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
-    if ((*MolWalker)->ActiveFlag) {
-      double * FullMatrix = ReturnFullMatrixforSymmetric((*MolWalker)->cell_size);
+  double ShortestDistance = 0.;
+  BoundaryTriangleSet *ShortestTriangle = NULL;
+  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
+    if ((*MolWalker)->ActiveFlag) {
+      double * FullMatrix = ReturnFullMatrixforSymmetric(World::get()->cell_size);
       double * FullInverseMatrix = InverseMatrix(FullMatrix);
-      Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
-      atom *Walker = (*MolWalker)->start;
-      while (Walker->next != (*MolWalker)->end) {
-        Walker = Walker->next;
-        Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl;
+      DoLog(2) && (Log() << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl);
+      atom *Walker = (*MolWalker)->start;
+      while (Walker->next != (*MolWalker)->end) {
+        Walker = Walker->next;
+        DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
         if ((type == NULL) || (Walker->type == type)) {
           periodicX.CopyVector(Walker->node);
           periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
           // go through every range in xyz and get distance
+          ShortestDistance = -1.;
           for (n[0]=-ranges[0]; n[0] <= ranges[0]; n[0]++)
             for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
@@ -320 +333 @@
                 checkX.AddVector(&periodicX);
                 checkX.MatrixMultiplication(FullMatrix);
-                triangle = Surface->FindClosestTriangleToPoint(&checkX, LC );
-                if (triangle != NULL) {
-                  distance = DistanceToTrianglePlane(&checkX, triangle);
-                  outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> (Walker, triangle) ) );
+                TriangleIntersectionList Intersections(&checkX,Surface,LC);
+                distance = Intersections.GetSmallestDistance();
+                triangle = Intersections.GetClosestTriangle();
+                if ((ShortestDistance == -1.) || (distance < ShortestDistance)) {
+                  ShortestDistance = distance;
+                  ShortestTriangle = triangle;
                 }
-          }
+              }
+          // insert
+          outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(ShortestDistance, pair<atom *, BoundaryTriangleSet*> (Walker, ShortestTriangle) ) );
+          //Log() << Verbose(1) << "INFO: Inserting " << Walker << " with distance " << ShortestDistance << " to " << *ShortestTriangle << "." << endl;
         }
       }
@@ -335 +353 @@
 };
 
-/** Returns the start of the bin for a given value.
+/** Returns the index of the bin for a given value.
  * \param value value whose bin to look for
  * \param BinWidth width of bin
  * \param BinStart first bin
  */
-double GetBin ( const double value, const double BinWidth, const double BinStart )
-{
-  double bin =(double) (floor((value - BinStart)/BinWidth));
-  return (bin*BinWidth+BinStart);
+int GetBin ( const double value, const double BinWidth, const double BinStart )
+{
+  Info FunctionInfo(__func__);
+  int bin =(int) (floor((value - BinStart)/BinWidth));
+  return (bin);
 };
 
@@ -353 +372 @@
 void OutputCorrelation( ofstream * const file, const BinPairMap * const map )
 {
-  *file << "# BinStart\tCount" << endl;
+  Info FunctionInfo(__func__);
+  *file << "BinStart\tCount" << endl;
   for (BinPairMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
-    *file << runner->first << "\t" << runner->second << endl;
+    *file << setprecision(8) << runner->first << "\t" << runner->second << endl;
   }
 };
@@ -365 +385 @@
 void OutputPairCorrelation( ofstream * const file, const PairCorrelationMap * const map )
 {
-  *file << "# BinStart\tAtom1\tAtom2" << endl;
+  Info FunctionInfo(__func__);
+  *file << "BinStart\tAtom1\tAtom2" << endl;
   for (PairCorrelationMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
-    *file << runner->first << "\t" << *(runner->second.first) << "\t" << *(runner->second.second) << endl;
+    *file << setprecision(8) << runner->first << "\t" << *(runner->second.first) << "\t" << *(runner->second.second) << endl;
   }
 };
@@ -377 +398 @@
 void OutputCorrelationToPoint( ofstream * const file, const CorrelationToPointMap * const map )
 {
-  *file << "# BinStart\tAtom::x[i]-point.x[i]" << endl;
+  Info FunctionInfo(__func__);
+  *file << "BinStart\tAtom::x[i]-point.x[i]" << endl;
   for (CorrelationToPointMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
     *file << runner->first;
     for (int i=0;i<NDIM;i++)
-      *file << "\t" << (runner->second.first->node->x[i] - runner->second.second->x[i]);
+      *file << "\t" << setprecision(8) << (runner->second.first->node->x[i] - runner->second.second->x[i]);
     *file << endl;
   }
@@ -392 +414 @@
 void OutputCorrelationToSurface( ofstream * const file, const CorrelationToSurfaceMap * const map )
 {
-  *file << "# BinStart\tTriangle" << endl;
-  for (CorrelationToSurfaceMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
-    *file << runner->first << "\t" << *(runner->second.second) << endl;
-  }
-};
-
+  Info FunctionInfo(__func__);
+  *file << "BinStart\tTriangle" << endl;
+  if (!map->empty())
+    for (CorrelationToSurfaceMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
+      *file << setprecision(8) << runner->first << "\t" << *(runner->second.first) << "\t" << *(runner->second.second) << endl;
+    }
+};
+