Changes in src/analysis_correlation.cpp [d74077:952f38]

File:

• src/analysis_correlation.cpp (modified) (11 diffs)

src/analysis_correlation.cpp

@@ -11 +11 @@
 #include <iomanip>
 
-#include "BoundaryTriangleSet.hpp"
 #include "analysis_correlation.hpp"
 #include "element.hpp"
-#include "info.hpp"
-#include "log.hpp"
+#include "Helpers/Info.hpp"
+#include "Helpers/Log.hpp"
 #include "molecule.hpp"
 #include "tesselation.hpp"
 #include "tesselationhelpers.hpp"
 #include "triangleintersectionlist.hpp"
-#include "vector.hpp"
-#include "Matrix.hpp"
-#include "verbose.hpp"
+#include "LinearAlgebra/Vector.hpp"
+#include "LinearAlgebra/Matrix.hpp"
+#include "Helpers/Verbose.hpp"
 #include "World.hpp"
 #include "Box.hpp"
@@ -75 +74 @@
           if ((*iter)->getId() < (*runner)->getId()){
             for (set <pair<element *, element *> >::iterator PairRunner = PairsOfElements.begin(); PairRunner != PairsOfElements.end(); ++PairRunner)
-              if ((PairRunner->first == (**iter).getType()) && (PairRunner->second == (**runner).getType())) {
-                distance = domain.periodicDistance((*iter)->getPosition(),(*runner)->getPosition());
+              if ((PairRunner->first == (**iter).type) && (PairRunner->second == (**runner).type)) {
+                distance = domain.periodicDistance(*(*iter)->node,*(*runner)->node);
                 //Log() << Verbose(1) <<"Inserting " << *(*iter) << " and " << *(*runner) << endl;
                 outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> ((*iter), (*runner)) ) );
@@ -138 +137 @@
     for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
       DoLog(3) && (Log() << Verbose(3) << "Current atom is " << **iter << "." << endl);
-      periodicX = FullInverseMatrix * ((*iter)->getPosition()); // x now in [0,1)^3
+      periodicX = FullInverseMatrix * (*(*iter)->node); // 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]++)
@@ -150 +149 @@
                   if ((*iter)->getId() < (*runner)->getId()){
                     for (set <pair<element *, element *> >::iterator PairRunner = PairsOfElements.begin(); PairRunner != PairsOfElements.end(); ++PairRunner)
-                      if ((PairRunner->first == (**iter).getType()) && (PairRunner->second == (**runner).getType())) {
-                        periodicOtherX = FullInverseMatrix * ((*runner)->getPosition()); // x now in [0,1)^3
+                      if ((PairRunner->first == (**iter).type) && (PairRunner->second == (**runner).type)) {
+                        periodicOtherX = FullInverseMatrix * (*(*runner)->node); // 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]++)
@@ -197 +196 @@
       DoLog(3) && (Log() << Verbose(3) << "Current atom is " << **iter << "." << endl);
       for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
-        if ((*type == NULL) || ((*iter)->getType() == *type)) {
-          distance = domain.periodicDistance((*iter)->getPosition(),*point);
+        if ((*type == NULL) || ((*iter)->type == *type)) {
+          distance = domain.periodicDistance(*(*iter)->node,*point);
           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) ) );
@@ -238 +237 @@
       DoLog(3) && (Log() << Verbose(3) << "Current atom is " << **iter << "." << endl);
       for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
-        if ((*type == NULL) || ((*iter)->getType() == *type)) {
-          periodicX = FullInverseMatrix * ((*iter)->getPosition()); // x now in [0,1)^3
+        if ((*type == NULL) || ((*iter)->type == *type)) {
+          periodicX = FullInverseMatrix * (*(*iter)->node); // 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]++)
@@ -285 +284 @@
       DoLog(3) && (Log() << Verbose(3) << "\tCurrent atom is " << *(*iter) << "." << endl);
       for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
-        if ((*type == NULL) || ((*iter)->getType() == *type)) {
-          TriangleIntersectionList Intersections((*iter)->getPosition(),Surface,LC);
+        if ((*type == NULL) || ((*iter)->type == *type)) {
+          TriangleIntersectionList Intersections((*iter)->node,Surface,LC);
           distance = Intersections.GetSmallestDistance();
           triangle = Intersections.GetClosestTriangle();
@@ -336 +335 @@
       DoLog(3) && (Log() << Verbose(3) << "Current atom is " << **iter << "." << endl);
       for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
-        if ((*type == NULL) || ((*iter)->getType() == *type)) {
-          periodicX = FullInverseMatrix * ((*iter)->getPosition()); // x now in [0,1)^3
+        if ((*type == NULL) || ((*iter)->type == *type)) {
+          periodicX = FullInverseMatrix * (*(*iter)->node); // x now in [0,1)^3
           // go through every range in xyz and get distance
           ShortestDistance = -1.;
@@ -344 +343 @@
               for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
                 checkX = FullMatrix * (Vector(n[0], n[1], n[2]) + periodicX);
-                TriangleIntersectionList Intersections(checkX,Surface,LC);
+                TriangleIntersectionList Intersections(&checkX,Surface,LC);
                 distance = Intersections.GetSmallestDistance();
                 triangle = Intersections.GetClosestTriangle();
@@ -412 +411 @@
     *file << runner->first;
     for (int i=0;i<NDIM;i++)
-      *file << "\t" << setprecision(8) << (runner->second.first->at(i) - runner->second.second->at(i));
+      *file << "\t" << setprecision(8) << (runner->second.first->node->at(i) - runner->second.second->at(i));
     *file << endl;
   }
@@ -427 +426 @@
   if (!map->empty())
     for (CorrelationToSurfaceMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
-      *file << setprecision(8) << runner->first << "\t";
-      *file << *(runner->second.first) << "\t";
-      *file << *(runner->second.second) << endl;
-    }
-};
-
+      *file << setprecision(8) << runner->first << "\t" << *(runner->second.first) << "\t" << *(runner->second.second) << endl;
+    }
+};
+