Changeset 1f591b for molecuilder/src/molecule_dynamics.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_dynamics.cpp (modified) (4 diffs)

molecuilder/src/molecule_dynamics.cpp

@@ -39 +39 @@
     // determine normalized trajectories direction vector (n1, n2)
     Sprinter = Params.PermutationMap[Walker->nr];   // find first target point
-    trajectory1.CopyVector(&Sprinter->Trajectory.R.at(Params.endstep));
-    trajectory1.SubtractVector(&Walker->Trajectory.R.at(Params.startstep));
+    trajectory1 = Sprinter->Trajectory.R.at(Params.endstep) - Walker->Trajectory.R.at(Params.startstep);
     trajectory1.Normalize();
     Norm1 = trajectory1.Norm();
     Sprinter = Params.PermutationMap[Runner->nr];   // find second target point
-    trajectory2.CopyVector(&Sprinter->Trajectory.R.at(Params.endstep));
-    trajectory2.SubtractVector(&Runner->Trajectory.R.at(Params.startstep));
+    trajectory2 = Sprinter->Trajectory.R.at(Params.endstep) - Runner->Trajectory.R.at(Params.startstep);
     trajectory2.Normalize();
     Norm2 = trajectory1.Norm();
     // check whether either is zero()
     if ((Norm1 < MYEPSILON) && (Norm2 < MYEPSILON)) {
-      tmp = Walker->Trajectory.R.at(Params.startstep).Distance(&Runner->Trajectory.R.at(Params.startstep));
+      tmp = Walker->Trajectory.R.at(Params.startstep).Distance(Runner->Trajectory.R.at(Params.startstep));
     } else if (Norm1 < MYEPSILON) {
       Sprinter = Params.PermutationMap[Walker->nr];   // find first target point
-      trajectory1.CopyVector(&Sprinter->Trajectory.R.at(Params.endstep));  // copy first offset
-      trajectory1.SubtractVector(&Runner->Trajectory.R.at(Params.startstep));  // subtract second offset
-      trajectory2.Scale( trajectory1.ScalarProduct(&trajectory2) ); // trajectory2 is scaled to unity, hence we don't need to divide by anything
-      trajectory1.SubtractVector(&trajectory2);   // project the part in norm direction away
+      trajectory1 = Sprinter->Trajectory.R.at(Params.endstep) - Runner->Trajectory.R.at(Params.startstep);
+      trajectory2 *= trajectory1.ScalarProduct(trajectory2); // trajectory2 is scaled to unity, hence we don't need to divide by anything
+      trajectory1 -= trajectory2;   // project the part in norm direction away
       tmp = trajectory1.Norm();  // remaining norm is distance
     } else if (Norm2 < MYEPSILON) {
       Sprinter = Params.PermutationMap[Runner->nr];   // find second target point
-      trajectory2.CopyVector(&Sprinter->Trajectory.R.at(Params.endstep));  // copy second offset
-      trajectory2.SubtractVector(&Walker->Trajectory.R.at(Params.startstep));  // subtract first offset
-      trajectory1.Scale( trajectory2.ScalarProduct(&trajectory1) ); // trajectory1 is scaled to unity, hence we don't need to divide by anything
-      trajectory2.SubtractVector(&trajectory1);   // project the part in norm direction away
+      trajectory2 = Sprinter->Trajectory.R.at(Params.endstep) - Walker->Trajectory.R.at(Params.startstep);  // copy second offset
+      trajectory1 *= trajectory2.ScalarProduct(trajectory1); // trajectory1 is scaled to unity, hence we don't need to divide by anything
+      trajectory2 -= trajectory1;   // project the part in norm direction away
       tmp = trajectory2.Norm();  // remaining norm is distance
-    } else if ((fabs(trajectory1.ScalarProduct(&trajectory2)/Norm1/Norm2) - 1.) < MYEPSILON) { // check whether they're linear dependent
+    } else if ((fabs(trajectory1.ScalarProduct(trajectory2)/Norm1/Norm2) - 1.) < MYEPSILON) { // check whether they're linear dependent
   //        Log() << Verbose(3) << "Both trajectories of " << *Walker << " and " << *Runner << " are linear dependent: ";
   //        Log() << Verbose(0) << trajectory1;
   //        Log() << Verbose(0) << " and ";
   //        Log() << Verbose(0) << trajectory2;
-      tmp = Walker->Trajectory.R.at(Params.startstep).Distance(&Runner->Trajectory.R.at(Params.startstep));
+      tmp = Walker->Trajectory.R.at(Params.startstep).Distance(Runner->Trajectory.R.at(Params.startstep));
   //        Log() << Verbose(0) << " with distance " << tmp << "." << endl;
     } else { // determine distance by finding minimum distance
@@ -97 +93 @@
   //        Log() << Verbose(0) << " with distance " << tmp << "." << endl;
       // test whether we really have the intersection (by checking on c_1 and c_2)
-      TestVector.CopyVector(&Runner->Trajectory.R.at(Params.startstep));
+      trajectory1.Scale(gsl_vector_get(x,0));
       trajectory2.Scale(gsl_vector_get(x,1));
-      TestVector.AddVector(&trajectory2);
       normal.Scale(gsl_vector_get(x,2));
-      TestVector.AddVector(&normal);
-      TestVector.SubtractVector(&Walker->Trajectory.R.at(Params.startstep));
-      trajectory1.Scale(gsl_vector_get(x,0));
-      TestVector.SubtractVector(&trajectory1);
+      TestVector = Runner->Trajectory.R.at(Params.startstep) + trajectory2 + normal
+                   - (Walker->Trajectory.R.at(Params.startstep) + trajectory1);
       if (TestVector.Norm() < MYEPSILON) {
   //          Log() << Verbose(2) << "Test: ok.\tDistance of " << tmp << " is correct." << endl;
@@ -173 +166 @@
     // first term: distance to target
     Runner = Params.PermutationMap[Walker->nr];   // find target point
-    tmp = (Walker->Trajectory.R.at(Params.startstep).Distance(&Runner->Trajectory.R.at(Params.endstep)));
+    tmp = (Walker->Trajectory.R.at(Params.startstep).Distance(Runner->Trajectory.R.at(Params.endstep)));
     tmp *= Params.IsAngstroem ? 1. : 1./AtomicLengthToAngstroem;
     result += Params.PenaltyConstants[0] * tmp;
@@ -232 +225 @@
     while(Runner->next != mol->end) {
       Runner = Runner->next;
-      Params.DistanceList[Walker->nr]->insert( DistancePair(Walker->Trajectory.R.at(Params.startstep).Distance(&Runner->Trajectory.R.at(Params.endstep)), Runner) );
+      Params.DistanceList[Walker->nr]->insert( DistancePair(Walker->Trajectory.R.at(Params.startstep).Distance(Runner->Trajectory.R.at(Params.endstep)), Runner) );
     }
   }