Changeset 0d111b for molecuilder/src/molecule_fragmentation.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/molecule_fragmentation.cpp (modified) (4 diffs)

molecuilder/src/molecule_fragmentation.cpp

@@ -1673 +1673 @@
     // remove bonds that are beyond bonddistance
     for(int i=NDIM;i--;)
-      Translationvector.x[i] = 0.;
+      Translationvector[i] = 0.;
     // scan all bonds
     Binder = first;
@@ -1680 +1680 @@
       Binder = Binder->next;
       for (int i=NDIM;i--;) {
-        tmp = fabs(Binder->leftatom->x.x[i] - Binder->rightatom->x.x[i]);
+        tmp = fabs(Binder->leftatom->x[i] - Binder->rightatom->x[i]);
         //Log() << Verbose(3) << "Checking " << i << "th distance of " << *Binder->leftatom << " to " << *Binder->rightatom << ": " << tmp << "." << endl;
         if (tmp > BondDistance) {
@@ -1694 +1694 @@
       // create translation vector from their periodically modified distance
       for (int i=NDIM;i--;) {
-        tmp = Binder->leftatom->x.x[i] - Binder->rightatom->x.x[i];
+        tmp = Binder->leftatom->x[i] - Binder->rightatom->x[i];
         if (fabs(tmp) > BondDistance)
-          Translationvector.x[i] = (tmp < 0) ? +1. : -1.;
+          Translationvector[i] = (tmp < 0) ? +1. : -1.;
       }
       Translationvector.MatrixMultiplication(matrix);
       //Log() << Verbose(3) << "Translation vector is ";
-      Translationvector.Output();
-      DoLog(0) && (Log() << Verbose(0) << endl);
+      Log() << Verbose(0) << Translationvector <<  endl;
       // apply to all atoms of first component via BFS
       for (int i=AtomCount;i--;)
@@ -1710 +1709 @@
         //Log() << Verbose (3) << "Current Walker is: " << *Walker << "." << endl;
         ColorList[Walker->nr] = black;    // mark as explored
-        Walker->x.AddVector(&Translationvector); // translate
+        Walker->x += Translationvector; // translate
         for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
           if ((*Runner) != Binder) {