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

File:

• src/molecule_fragmentation.cpp (modified) (9 diffs)

src/molecule_fragmentation.cpp

@@ -15 +15 @@
 #include "config.hpp"
 #include "element.hpp"
-#include "helpers.hpp"
+#include "Helpers/helpers.hpp"
 #include "lists.hpp"
-#include "verbose.hpp"
-#include "log.hpp"
+#include "Helpers/Verbose.hpp"
+#include "Helpers/Log.hpp"
 #include "molecule.hpp"
 #include "periodentafel.hpp"
 #include "World.hpp"
-#include "Matrix.hpp"
+#include "LinearAlgebra/Matrix.hpp"
 #include "Box.hpp"
 #include "stackclass.hpp"
@@ -451 +451 @@
       for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
     #ifdef ADDHYDROGEN
-        if ((*iter)->getType()->Z != 1) // skip hydrogen
+        if ((*iter)->type->Z != 1) // skip hydrogen
     #endif
         {
@@ -471 +471 @@
     for(molecule::const_iterator iter = begin(); iter != end(); ++iter) {
   #ifdef ADDHYDROGEN
-      if ((*iter)->getType()->Z != 1) // skip hydrogen
+      if ((*iter)->type->Z != 1) // skip hydrogen
   #endif
       {
@@ -880 +880 @@
   for (KeySet::iterator runner = Leaf->begin(); runner != Leaf->end(); runner++) {
     Runner = FindAtom((*runner));
-    if (Runner->getType()->Z != 1) { // skip all those added hydrogens when re-filling snake stack
+    if (Runner->type->Z != 1) { // skip all those added hydrogens when re-filling snake stack
       if (ShortestPathList[(*runner)] > SP) {  // remove the oldest one with longest shortest path
         SP = ShortestPathList[(*runner)];
@@ -969 +969 @@
     ++iter;
 #ifdef ADDHYDROGEN
-    while ((iter != Leaf->end()) && ((*iter)->getType()->Z == 1)){ // skip added hydrogen
+    while ((iter != Leaf->end()) && ((*iter)->type->Z == 1)){ // skip added hydrogen
       iter++;
     }
@@ -1347 +1347 @@
         if ((RestrictedKeySet.find(OtherWalker->nr) != RestrictedKeySet.end())
   #ifdef ADDHYDROGEN
-         && (OtherWalker->getType()->Z != 1)
+         && (OtherWalker->type->Z != 1)
   #endif
                                                               ) {  // skip hydrogens and restrict to fragment
@@ -1741 +1741 @@
         Binder = (*BondRunner);
         for (int i=NDIM;i--;) {
-          tmp = fabs(Binder->leftatom->at(i) - Binder->rightatom->at(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) {
@@ -1755 +1755 @@
       // create translation vector from their periodically modified distance
       for (int i=NDIM;i--;) {
-        tmp = Binder->leftatom->at(i) - Binder->rightatom->at(i);
+        tmp = Binder->leftatom->x[i] - Binder->rightatom->x[i];
         if (fabs(tmp) > BondDistance)
           Translationvector[i] = (tmp < 0) ? +1. : -1.;
@@ -1770 +1770 @@
         //Log() << Verbose (3) << "Current Walker is: " << *Walker << "." << endl;
         ColorList[Walker->nr] = black;    // mark as explored
-        *Walker += Translationvector; // translate
+        Walker->x += Translationvector; // translate
         for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
           if ((*Runner) != Binder) {