Changeset 0d111b for molecuilder/src/analysis_correlation.cpp

Timestamp:

Apr 29, 2010, 1:55:21 PM (16 years ago)

Author:

Tillmann Crueger <crueger@…>

Children:

070651, 5d1a94

Parents:

90c4460 (diff), 32842d8 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'VectorRefactoring' into StructureRefactoring

Conflicts:

molecuilder/src/Legacy/oldmenu.cpp
molecuilder/src/Makefile.am
molecuilder/src/analysis_correlation.cpp
molecuilder/src/boundary.cpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/ellipsoid.cpp
molecuilder/src/linkedcell.cpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/tesselation.cpp
molecuilder/src/tesselationhelpers.cpp
molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp
molecuilder/src/unittests/bondgraphunittest.cpp
molecuilder/src/vector.cpp
molecuilder/src/vector.hpp

File:

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

molecuilder/src/analysis_correlation.cpp

@@ -57 +57 @@
                 if (Walker->nr < OtherWalker->nr)
                   if ((type2 == NULL) || (OtherWalker->type == type2)) {
-                    distance = Walker->node->PeriodicDistance(OtherWalker->node, World::getInstance().getDomain());
+                    distance = Walker->node->PeriodicDistance(*OtherWalker->node, World::getInstance().getDomain());
                     //Log() << Verbose(1) <<"Inserting " << *Walker << " and " << *OtherWalker << endl;
                     outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> (Walker, OtherWalker) ) );
@@ -106 +106 @@
         DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
         if ((type1 == NULL) || (Walker->type == type1)) {
-          periodicX.CopyVector(Walker->node);
+          periodicX = *(Walker->node);
           periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
           // go through every range in xyz and get distance
@@ -112 +112 @@
             for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
               for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
-                checkX.Init(n[0], n[1], n[2]);
-                checkX.AddVector(&periodicX);
+                checkX = Vector(n[0], n[1], n[2]) + periodicX;
                 checkX.MatrixMultiplication(FullMatrix);
                 for (MoleculeList::const_iterator MolOtherWalker = MolWalker; MolOtherWalker != molecules->ListOfMolecules.end(); MolOtherWalker++)
@@ -124 +123 @@
                       if (Walker->nr < OtherWalker->nr)
                         if ((type2 == NULL) || (OtherWalker->type == type2)) {
-                          periodicOtherX.CopyVector(OtherWalker->node);
+                          periodicOtherX = *(OtherWalker->node);
                           periodicOtherX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
                           // go through every range in xyz and get distance
@@ -130 +129 @@
                             for (Othern[1]=-ranges[1]; Othern[1] <= ranges[1]; Othern[1]++)
                               for (Othern[2]=-ranges[2]; Othern[2] <= ranges[2]; Othern[2]++) {
-                                checkOtherX.Init(Othern[0], Othern[1], Othern[2]);
-                                checkOtherX.AddVector(&periodicOtherX);
+                                checkOtherX = Vector(Othern[0], Othern[1], Othern[2]) + periodicOtherX;
                                 checkOtherX.MatrixMultiplication(FullMatrix);
-                                distance = checkX.Distance(&checkOtherX);
+                                distance = checkX.Distance(checkOtherX);
                                 //Log() << Verbose(1) <<"Inserting " << *Walker << " and " << *OtherWalker << endl;
                                 outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> (Walker, OtherWalker) ) );
@@ -176 +174 @@
         DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
         if ((type == NULL) || (Walker->type == type)) {
-          distance = Walker->node->PeriodicDistance(point, World::getInstance().getDomain());
+          distance = Walker->node->PeriodicDistance(*point, World::getInstance().getDomain());
           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) ) );
@@ -218 +216 @@
         DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
         if ((type == NULL) || (Walker->type == type)) {
-          periodicX.CopyVector(Walker->node);
+          periodicX = *(Walker->node);
           periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
           // go through every range in xyz and get distance
@@ -224 +222 @@
             for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
               for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
-                checkX.Init(n[0], n[1], n[2]);
-                checkX.AddVector(&periodicX);
+                checkX = Vector(n[0], n[1], n[2]) + periodicX;
                 checkX.MatrixMultiplication(FullMatrix);
-                distance = checkX.Distance(point);
+                distance = checkX.Distance(*point);
                 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) ) );
@@ -322 +319 @@
         DoLog(3) && (Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl);
         if ((type == NULL) || (Walker->type == type)) {
-          periodicX.CopyVector(Walker->node);
+          periodicX = *(Walker->node);
           periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
           // go through every range in xyz and get distance
@@ -329 +326 @@
             for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
               for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
-                checkX.Init(n[0], n[1], n[2]);
-                checkX.AddVector(&periodicX);
+                checkX = Vector(n[0], n[1], n[2]) + periodicX;
                 checkX.MatrixMultiplication(FullMatrix);
                 TriangleIntersectionList Intersections(&checkX,Surface,LC);
@@ -402 +398 @@
     *file << runner->first;
     for (int i=0;i<NDIM;i++)
-      *file << "\t" << setprecision(8) << (runner->second.first->node->x[i] - runner->second.second->x[i]);
+      *file << "\t" << setprecision(8) << (runner->second.first->node->at(i) - runner->second.second->at(i));
     *file << endl;
   }