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

File:

• src/molecule_graph.cpp (modified) (3 diffs)

src/molecule_graph.cpp

@@ -18 +18 @@
 #include "defs.hpp"
 #include "element.hpp"
-#include "Helpers/helpers.hpp"
-#include "Helpers/Info.hpp"
+#include "helpers.hpp"
+#include "info.hpp"
 #include "linkedcell.hpp"
 #include "lists.hpp"
-#include "Helpers/Verbose.hpp"
-#include "Helpers/Log.hpp"
+#include "verbose.hpp"
+#include "log.hpp"
 #include "molecule.hpp"
 #include "World.hpp"
 #include "Helpers/fast_functions.hpp"
 #include "Helpers/Assert.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "Matrix.hpp"
 #include "Box.hpp"
 #include "stackclass.hpp"
@@ -184 +184 @@
                           //Log() << Verbose(1) << "Checking distance " << OtherWalker->x.PeriodicDistanceSquared(&(Walker->x), cell_size) << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
                           (BG->*minmaxdistance)(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
-                          const double distance = domain.periodicDistanceSquared(OtherWalker->x,Walker->x);
+                          const double distance = domain.periodicDistanceSquared(OtherWalker->getPosition(),Walker->getPosition());
                           const bool status = (distance <= MaxDistance * MaxDistance) && (distance >= MinDistance * MinDistance);
 //                          Log() << Verbose(1) << "MinDistance is " << MinDistance << " and MaxDistance is " << MaxDistance << "." << endl;
@@ -737 +737 @@
         OtherAtom = (*Runner)->GetOtherAtom(Walker);
 #ifdef ADDHYDROGEN
-        if (OtherAtom->type->Z != 1) {
+        if (OtherAtom->getType()->Z != 1) {
 #endif
         DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);