Changes in src/analysis_correlation.cpp [952f38:e5c0a1]

File:

• src/analysis_correlation.cpp (modified) (15 diffs)

src/analysis_correlation.cpp

@@ -13 +13 @@
 #include "analysis_correlation.hpp"
 #include "element.hpp"
-#include "Helpers/Info.hpp"
-#include "Helpers/Log.hpp"
+#include "info.hpp"
+#include "log.hpp"
 #include "molecule.hpp"
 #include "tesselation.hpp"
 #include "tesselationhelpers.hpp"
 #include "triangleintersectionlist.hpp"
-#include "LinearAlgebra/Vector.hpp"
-#include "LinearAlgebra/Matrix.hpp"
-#include "Helpers/Verbose.hpp"
+#include "vector.hpp"
+#include "Matrix.hpp"
+#include "verbose.hpp"
 #include "World.hpp"
 #include "Box.hpp"
@@ -32 +32 @@
  * \return Map of doubles with values the pair of the two atoms.
  */
-PairCorrelationMap *PairCorrelation(std::vector<molecule *> &molecules, const std::vector<element *> &elements)
+PairCorrelationMap *PairCorrelation(std::vector<molecule *> &molecules, const std::vector<const element *> &elements)
 {
   Info FunctionInfo(__func__);
@@ -47 +47 @@
 
   // create all possible pairs of elements
-  set <pair<element *, element *> > PairsOfElements;
+  set <pair<const element *,const element *> > PairsOfElements;
   if (elements.size() >= 2) {
-    for (vector<element *>::const_iterator type1 = elements.begin(); type1 != elements.end(); ++type1)
-      for (vector<element *>::const_iterator type2 = elements.begin(); type2 != elements.end(); ++type2)
+    for (vector<const element *>::const_iterator type1 = elements.begin(); type1 != elements.end(); ++type1)
+      for (vector<const element *>::const_iterator type2 = elements.begin(); type2 != elements.end(); ++type2)
         if (type1 != type2) {
-          PairsOfElements.insert( pair<element *, element*>(*type1,*type2) );
-          DoLog(1) && (Log() << Verbose(1) << "Creating element pair " << (*type1)->symbol << " and " << (*type2)->symbol << "." << endl);
+          PairsOfElements.insert( make_pair(*type1,*type2) );
+          DoLog(1) && (Log() << Verbose(1) << "Creating element pair " << *(*type1) << " and " << *(*type2) << "." << endl);
         }
   } else if (elements.size() == 1) { // one to all are valid
-    element *elemental = *elements.begin();
-    PairsOfElements.insert( pair<element *, element*>(elemental,(element *)NULL) );
-    PairsOfElements.insert( pair<element *, element*>((element *)NULL,elemental) );
+    const element *elemental = *elements.begin();
+    PairsOfElements.insert( pair<const element *,const element*>(elemental,0) );
+    PairsOfElements.insert( pair<const element *,const element*>(0,elemental) );
   } else { // all elements valid
     PairsOfElements.insert( pair<element *, element*>((element *)NULL, (element *)NULL) );
@@ -73 +73 @@
           DoLog(3) && (Log() << Verbose(3) << "Current otheratom is " << **runner << "." << endl);
           if ((*iter)->getId() < (*runner)->getId()){
-            for (set <pair<element *, element *> >::iterator PairRunner = PairsOfElements.begin(); PairRunner != PairsOfElements.end(); ++PairRunner)
+            for (set <pair<const element *,const element *> >::iterator PairRunner = PairsOfElements.begin(); PairRunner != PairsOfElements.end(); ++PairRunner)
               if ((PairRunner->first == (**iter).type) && (PairRunner->second == (**runner).type)) {
                 distance = domain.periodicDistance(*(*iter)->node,*(*runner)->node);
@@ -94 +94 @@
  * \return Map of doubles with values the pair of the two atoms.
  */
-PairCorrelationMap *PeriodicPairCorrelation(std::vector<molecule *> &molecules, const std::vector<element *> &elements, const int ranges[NDIM] )
+PairCorrelationMap *PeriodicPairCorrelation(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const int ranges[NDIM] )
 {
   Info FunctionInfo(__func__);
@@ -114 +114 @@
 
   // create all possible pairs of elements
-  set <pair<element *, element *> > PairsOfElements;
+  set <pair<const element *,const element *> > PairsOfElements;
   if (elements.size() >= 2) {
-    for (vector<element *>::const_iterator type1 = elements.begin(); type1 != elements.end(); ++type1)
-      for (vector<element *>::const_iterator type2 = elements.begin(); type2 != elements.end(); ++type2)
+    for (vector<const element *>::const_iterator type1 = elements.begin(); type1 != elements.end(); ++type1)
+      for (vector<const element *>::const_iterator type2 = elements.begin(); type2 != elements.end(); ++type2)
         if (type1 != type2) {
-          PairsOfElements.insert( pair<element *, element*>(*type1,*type2) );
-          DoLog(1) && (Log() << Verbose(1) << "Creating element pair " << (*type1)->symbol << " and " << (*type2)->symbol << "." << endl);
+          PairsOfElements.insert( make_pair(*type1,*type2) );
+          DoLog(1) && (Log() << Verbose(1) << "Creating element pair " << *(*type1) << " and " << *(*type2) << "." << endl);
         }
   } else if (elements.size() == 1) { // one to all are valid
-    element *elemental = *elements.begin();
-    PairsOfElements.insert( pair<element *, element*>(elemental,(element *)NULL) );
-    PairsOfElements.insert( pair<element *, element*>((element *)NULL,elemental) );
+    const element *elemental = *elements.begin();
+    PairsOfElements.insert( pair<const element *,const element*>(elemental,0) );
+    PairsOfElements.insert( pair<const element *,const element*>(0,elemental) );
   } else { // all elements valid
     PairsOfElements.insert( pair<element *, element*>((element *)NULL, (element *)NULL) );
@@ -148 +148 @@
                   DoLog(3) && (Log() << Verbose(3) << "Current otheratom is " << **runner << "." << endl);
                   if ((*iter)->getId() < (*runner)->getId()){
-                    for (set <pair<element *, element *> >::iterator PairRunner = PairsOfElements.begin(); PairRunner != PairsOfElements.end(); ++PairRunner)
+                    for (set <pair<const element *,const element *> >::iterator PairRunner = PairsOfElements.begin(); PairRunner != PairsOfElements.end(); ++PairRunner)
                       if ((PairRunner->first == (**iter).type) && (PairRunner->second == (**runner).type)) {
                         periodicOtherX = FullInverseMatrix * (*(*runner)->node); // x now in [0,1)^3
@@ -177 +177 @@
  * \return Map of dobules with values as pairs of atom and the vector
  */
-CorrelationToPointMap *CorrelationToPoint(std::vector<molecule *> &molecules, const std::vector<element *> &elements, const Vector *point )
+CorrelationToPointMap *CorrelationToPoint(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Vector *point )
 {
   Info FunctionInfo(__func__);
@@ -195 +195 @@
     for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
       DoLog(3) && (Log() << Verbose(3) << "Current atom is " << **iter << "." << endl);
-      for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
+      for (vector<const element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
         if ((*type == NULL) || ((*iter)->type == *type)) {
           distance = domain.periodicDistance(*(*iter)->node,*point);
@@ -214 +214 @@
  * \return Map of dobules with values as pairs of atom and the vector
  */
-CorrelationToPointMap *PeriodicCorrelationToPoint(std::vector<molecule *> &molecules, const std::vector<element *> &elements, const Vector *point, const int ranges[NDIM] )
+CorrelationToPointMap *PeriodicCorrelationToPoint(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Vector *point, const int ranges[NDIM] )
 {
   Info FunctionInfo(__func__);
@@ -236 +236 @@
     for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
       DoLog(3) && (Log() << Verbose(3) << "Current atom is " << **iter << "." << endl);
-      for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
+      for (vector<const element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
         if ((*type == NULL) || ((*iter)->type == *type)) {
           periodicX = FullInverseMatrix * (*(*iter)->node); // x now in [0,1)^3
@@ -262 +262 @@
  * \return Map of doubles with values as pairs of atom and the BoundaryTriangleSet that's closest
  */
-CorrelationToSurfaceMap *CorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<element *> &elements, const Tesselation * const Surface, const LinkedCell *LC )
+CorrelationToSurfaceMap *CorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell *LC )
 {
   Info FunctionInfo(__func__);
@@ -283 +283 @@
     for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
       DoLog(3) && (Log() << Verbose(3) << "\tCurrent atom is " << *(*iter) << "." << endl);
-      for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
+      for (vector<const element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
         if ((*type == NULL) || ((*iter)->type == *type)) {
           TriangleIntersectionList Intersections((*iter)->node,Surface,LC);
@@ -308 +308 @@
  * \return Map of doubles with values as pairs of atom and the BoundaryTriangleSet that's closest
  */
-CorrelationToSurfaceMap *PeriodicCorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<element *> &elements, const Tesselation * const Surface, const LinkedCell *LC, const int ranges[NDIM] )
+CorrelationToSurfaceMap *PeriodicCorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell *LC, const int ranges[NDIM] )
 {
   Info FunctionInfo(__func__);
@@ -334 +334 @@
     for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
       DoLog(3) && (Log() << Verbose(3) << "Current atom is " << **iter << "." << endl);
-      for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
+      for (vector<const element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
         if ((*type == NULL) || ((*iter)->type == *type)) {
           periodicX = FullInverseMatrix * (*(*iter)->node); // x now in [0,1)^3