Changeset 1f591b for molecuilder/src/molecule_geometry.cpp

Timestamp:

Apr 13, 2010, 1:22:42 PM (16 years ago)

Author:

Tillmann Crueger <crueger@…>

Children:

e7ea64

Parents:

0f55b2

Message:

Prepared interface of Vector Class for transition to VectorComposites

File:

• molecuilder/src/molecule_geometry.cpp (modified) (15 diffs)

molecuilder/src/molecule_geometry.cpp

@@ -30 +30 @@
 
   // go through all atoms
-  ActOnAllVectors( &Vector::SubtractVector, Center);
+  ActOnAllVectors( &Vector::SubtractVector, *Center);
   ActOnAllVectors( &Vector::WrapPeriodically, (const double *)M, (const double *)Minv);
 
@@ -86 +86 @@
 //    Log() << Verbose(0) << endl;
     min->Scale(-1.);
-    max->AddVector(min);
+    (*max) += (*min);
     Translate(min);
     Center.Zero();
@@ -109 +109 @@
       ptr = ptr->next;
       Num++;
-      Center.AddVector(&ptr->x);
+      Center += ptr->x;
     }
     Center.Scale(-1./Num); // divide through total number (and sign for direction)
@@ -133 +133 @@
       ptr = ptr->next;
       Num += 1.;
-      tmp.CopyVector(&ptr->x);
-      a->AddVector(&tmp);
+      tmp = ptr->x;
+      (*a) += tmp;
     }
     a->Scale(1./Num); // divide through total mass (and sign for direction)
@@ -158 +158 @@
       ptr = ptr->next;
       Num += ptr->type->mass;
-      tmp.CopyVector(&ptr->x);
-      tmp.Scale(ptr->type->mass);  // scale by mass
-      a->AddVector(&tmp);
+      tmp = ptr->type->mass * ptr->x;
+      (*a) += tmp;
     }
     a->Scale(-1./Num); // divide through total mass (and sign for direction)
@@ -186 +185 @@
 void molecule::CenterAtVector(Vector *newcenter)
 {
-  Center.CopyVector(newcenter);
+  Center = *newcenter;
 };
 
@@ -215 +214 @@
     ptr = ptr->next;
     for (int j=0;j<MDSteps;j++)
-      ptr->Trajectory.R.at(j).Translate(trans);
-    ptr->x.Translate(trans);
+      ptr->Trajectory.R.at(j).Translate(*trans);
+    ptr->x.Translate(*trans);
   }
 };
@@ -230 +229 @@
 
   // go through all atoms
-  ActOnAllVectors( &Vector::SubtractVector, trans);
+  ActOnAllVectors( &Vector::SubtractVector, *trans);
   ActOnAllVectors( &Vector::WrapPeriodically, (const double *)M, (const double *)Minv);
 
@@ -243 +242 @@
 void molecule::Mirror(const Vector *n)
 {
-  ActOnAllVectors( &Vector::Mirror, n );
+  ActOnAllVectors( &Vector::Mirror, *n );
 };
 
@@ -266 +265 @@
       if (Walker->type->Z != 1) {
 #endif
-        Testvector.CopyVector(&Walker->x);
+        Testvector = Walker->x;
         Testvector.MatrixMultiplication(inversematrix);
         Translationvector.Zero();
@@ -283 +282 @@
             }
         }
-        Testvector.AddVector(&Translationvector);
+        Testvector += Translationvector;
         Testvector.MatrixMultiplication(matrix);
-        Center.AddVector(&Testvector);
+        Center += Testvector;
         Log() << Verbose(1) << "vector is: " << Testvector << endl;
 #ifdef ADDHYDROGEN
@@ -291 +290 @@
         for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
           if ((*Runner)->GetOtherAtom(Walker)->type->Z == 1) {
-            Testvector.CopyVector(&(*Runner)->GetOtherAtom(Walker)->x);
+            Testvector = (*Runner)->GetOtherAtom(Walker)->x;
             Testvector.MatrixMultiplication(inversematrix);
-            Testvector.AddVector(&Translationvector);
+            Testvector += Translationvector;
             Testvector.MatrixMultiplication(matrix);
-            Center.AddVector(&Testvector);
+            Center += Testvector;
             Log() << Verbose(1) << "Hydrogen vector is: " << Testvector << endl;
           }
@@ -329 +328 @@
   while (ptr->next != end) {
     ptr = ptr->next;
-    Vector x;
-    x.CopyVector(&ptr->x);
+    Vector x = ptr->x;
     //x.SubtractVector(CenterOfGravity);
     InertiaTensor[0] += ptr->type->mass*(x[1]*x[1] + x[2]*x[2]);
@@ -381 +379 @@
     while (ptr->next != end) {
       ptr = ptr->next;
-      Vector x;
-      x.CopyVector(&ptr->x);
+      Vector x = ptr->x;
       //x.SubtractVector(CenterOfGravity);
       InertiaTensor[0] += ptr->type->mass*(x[1]*x[1] + x[2]*x[2]);
@@ -492 +489 @@
     ptr = ptr->next;
     if (ptr->type == ((struct lsq_params *)params)->type) { // for specific type
-      c.CopyVector(&ptr->x);  // copy vector to temporary one
-      c.SubtractVector(&a);   // subtract offset vector
-      t = c.ScalarProduct(&b);           // get direction parameter
-      d.CopyVector(&b);       // and create vector
-      d.Scale(&t);
-      c.SubtractVector(&d);   // ... yielding distance vector
-      res += d.ScalarProduct((const Vector *)&d);        // add squared distance
+      c = ptr->x - a;
+      t = c.ScalarProduct(b);           // get direction parameter
+      d = t*b;       // and create vector
+      c -= d;   // ... yielding distance vector
+      res += d.ScalarProduct(d);        // add squared distance
     }
   }