Changes in src/builder.cpp [632bc3:68f03d]

File:

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

src/builder.cpp

@@ -1741 +1741 @@
                   DoLog(2) && (Log() << Verbose(2) << "found element " << first->type->name << endl);
                 for (int i=NDIM;i--;)
-                  first->x.x[i] = atof(argv[argptr+1+i]);
+                  first->x[i] = atof(argv[argptr+1+i]);
                 if (first->type != NULL) {
                   mol->AddAtom(first);  // add to molecule
@@ -2013 +2013 @@
                 first = World::getInstance().createAtom();
                 first->type = periode->FindElement(1);
-                first->x.Init(0.441, -0.143, 0.);
+                first->x = Vector(0.441, -0.143, 0.);
                 filler->AddAtom(first);
                 second = World::getInstance().createAtom();
                 second->type = periode->FindElement(1);
-                second->x.Init(-0.464, 1.137, 0.0);
+                second->x = Vector(-0.464, 1.137, 0.0);
                 filler->AddAtom(second);
                 third = World::getInstance().createAtom();
                 third->type = periode->FindElement(8);
-                third->x.Init(-0.464, 0.177, 0.);
+                third->x = Vector(-0.464, 0.177, 0.);
                 filler->AddAtom(third);
                 filler->AddBond(first, third, 1);
@@ -2186 +2186 @@
                     first = second;
                     second = first->next;
-                    if (first->x.DistanceSquared((const Vector *)&third->x) > tmp1*tmp1) // distance to first above radius ...
+                    if (first->x.DistanceSquared(third->x) > tmp1*tmp1) // distance to first above radius ...
                       mol->RemoveAtom(first);
                   }
@@ -2206 +2206 @@
                 DoLog(1) && (Log() << Verbose(1) << "Translating all ions by given vector." << endl);
                 for (int i=NDIM;i--;)
-                  x.x[i] = atof(argv[argptr+i]);
+                  x[i] = atof(argv[argptr+i]);
                 mol->Translate((const Vector *)&x);
                 argptr+=3;
@@ -2222 +2222 @@
                 DoLog(1) && (Log() << Verbose(1) << "Translating all ions periodically by given vector." << endl);
                 for (int i=NDIM;i--;)
-                  x.x[i] = atof(argv[argptr+i]);
+                  x[i] = atof(argv[argptr+i]);
                 mol->TranslatePeriodically((const Vector *)&x);
                 argptr+=3;
@@ -2245 +2245 @@
                 for (int i=0;i<NDIM;i++) {
                   j += i+1;
-                  x.x[i] = atof(argv[NDIM+i]);
+                  x[i] = atof(argv[NDIM+i]);
                   cell_size[j]*=factor[i];
                 }
@@ -2309 +2309 @@
                 for (int i=0;i<NDIM;i++) {
                   j += i+1;
-                  x.x[i] = atof(argv[argptr+i]);
-                  cell_size[j] += x.x[i]*2.;
+                  x[i] = atof(argv[argptr+i]);
+                  cell_size[j] += x[i]*2.;
                 }
                 mol->Translate((const Vector *)&x);
@@ -2468 +2468 @@
                     x.Zero();
                     y.Zero();
-                    y.x[abs(axis)-1] = cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] * abs(axis)/axis; // last term is for sign, first is for magnitude
+                    y[abs(axis)-1] = cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] * abs(axis)/axis; // last term is for sign, first is for magnitude
                     for (int i=1;i<faktor;i++) {  // then add this list with respective translation factor times
-                      x.AddVector(&y); // per factor one cell width further
+                      x += y; // per factor one cell width further
                       for (int k=count;k--;) { // go through every atom of the original cell
                         first = World::getInstance().createAtom(); // create a new body
-                        first->x.CopyVector(vectors[k]);  // use coordinate of original atom
-                        first->x.AddVector(&x);      // translate the coordinates
+                        first->x = (*vectors[k]) + x;
                         first->type = Elements[k];  // insert original element
                         mol->AddAtom(first);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
@@ -2484 +2483 @@
                     // correct cell size
                     if (axis < 0) { // if sign was negative, we have to translate everything
-                      x.Zero();
-                      x.AddVector(&y);
-                      x.Scale(-(faktor-1));
+                      x =(-(faktor-1)) * y;
                       mol->Translate(&x);
                     }
@@ -2554 +2551 @@
   ActionRegistry::purgeInstance();
   ActionHistory::purgeInstance();
+  Memory::getState();
 }
 
@@ -2619 +2617 @@
   cleanUp(configuration);
 
-  Memory::getState();
   return (0);
 }