Changes in src/molecule_dynamics.cpp [1513a74:920c70]

File:

• src/molecule_dynamics.cpp (modified) (10 diffs)

src/molecule_dynamics.cpp

@@ -10 +10 @@
 #include "config.hpp"
 #include "element.hpp"
+#include "info.hpp"
 #include "log.hpp"
 #include "memoryallocator.hpp"
@@ -189 +190 @@
 {
   stringstream zeile1, zeile2;
-  int *DoubleList = Calloc<int>(AtomCount, "PrintPermutationMap: *DoubleList");
+  int *DoubleList = new int[AtomCount];
+  for(int i=0;i<AtomCount;i++)
+    DoubleList[i] = 0;
   int doubles = 0;
   zeile1 << "PermutationMap: ";
@@ -203 +206 @@
   if (doubles >0)
     DoLog(2) && (Log() << Verbose(2) << "Found " << doubles << " Doubles." << endl);
-  Free(&DoubleList);
+  delete[](DoubleList);
 //  Log() << Verbose(2) << zeile1.str() << endl << zeile2.str() << endl;
 };
@@ -338 +341 @@
   double Potential, OldPotential, OlderPotential;
   struct EvaluatePotential Params;
-  Params.PermutationMap = Calloc<atom*>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.**PermutationMap");
-  Params.DistanceList = Malloc<DistanceMap*>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.**DistanceList");
-  Params.DistanceIterators = Malloc<DistanceMap::iterator>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.*DistanceIterators");
-  Params.DoubleList = Calloc<int>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.*DoubleList");
-  Params.StepList = Malloc<DistanceMap::iterator>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.*StepList");
+  Params.PermutationMap = new atom *[AtomCount];
+  Params.DistanceList = new DistanceMap *[AtomCount];
+  Params.DistanceIterators = new DistanceMap::iterator[AtomCount];
+  Params.DoubleList = new int[AtomCount];
+  Params.StepList = new DistanceMap::iterator[AtomCount];
   int round;
   atom *Walker = NULL, *Runner = NULL, *Sprinter = NULL;
   DistanceMap::iterator Rider, Strider;
+
+  // set to zero
+  for (int i=0;i<AtomCount;i++) {
+    Params.PermutationMap[i] = NULL;
+    Params.DoubleList[i] = 0;
+  }
 
   /// Minimise the potential
@@ -362 +371 @@
   DoLog(1) && (Log() << Verbose(1) << "Making the PermutationMap injective ... " << endl);
   MakeInjectivePermutation(this, Params);
-  Free(&Params.DoubleList);
+  delete[](Params.DoubleList);
 
   // argument minimise the constrained potential in this injective PermutationMap
@@ -444 +453 @@
   for (int i=AtomCount; i--;)
     Params.DistanceList[i]->clear();
-  Free(&Params.DistanceList);
-  Free(&Params.DistanceIterators);
+  delete[](Params.DistanceList);
+  delete[](Params.DistanceIterators);
   return ConstrainedPotential(Params);
 };
@@ -487 +496 @@
     MinimiseConstrainedPotential(PermutationMap, startstep, endstep, configuration.GetIsAngstroem());
   else {
-    PermutationMap = Malloc<atom *>(AtomCount, "molecule::LinearInterpolationBetweenConfiguration: **PermutationMap");
+    PermutationMap = new atom *[AtomCount];
     SetIndexedArrayForEachAtomTo( PermutationMap, &atom::nr );
   }
@@ -522 +531 @@
 
   // store the list to single step files
-  int *SortIndex = Malloc<int>(AtomCount, "molecule::LinearInterpolationBetweenConfiguration: *SortIndex");
+  int *SortIndex = new int[AtomCount];
   for (int i=AtomCount; i--; )
     SortIndex[i] = i;
   status = MoleculePerStep->OutputConfigForListOfFragments(&configuration, SortIndex);
+  delete[](SortIndex);
 
   // free and return
-  Free(&PermutationMap);
+  delete[](PermutationMap);
   delete(MoleculePerStep);
   return status;
@@ -548 +558 @@
 bool molecule::VerletForceIntegration(char *file, config &configuration)
 {
+  Info FunctionInfo(__func__);
   ifstream input(file);
   string token;
@@ -588 +599 @@
       ConstrainedPotentialEnergy = MinimiseConstrainedPotential(PermutationMap,configuration.DoConstrainedMD, 0, configuration.GetIsAngstroem());
       EvaluateConstrainedForces(configuration.DoConstrainedMD, 0, PermutationMap, &Force);
-      Free(&PermutationMap);
+      delete[](PermutationMap);
     }
 
     // and perform Verlet integration for each atom with position, velocity and force vector
     // check size of vectors
-    ActOnAllAtoms( &atom::ResizeTrajectory, MDSteps+10 );
-
-    ActOnAllAtoms( &atom::VelocityVerletUpdate, MDSteps, &configuration, &Force);
+    //ActOnAllAtoms( &atom::ResizeTrajectory, MDSteps+10 );
+
+    ActOnAllAtoms( &atom::VelocityVerletUpdate, MDSteps+1, &configuration, &Force);
   }
   // correct velocities (rather momenta) so that center of mass remains motionless
   Velocity.Zero();
   IonMass = 0.;
-  ActOnAllAtoms ( &atom::SumUpKineticEnergy, MDSteps, &IonMass, &Velocity );
+  ActOnAllAtoms ( &atom::SumUpKineticEnergy, MDSteps+1, &IonMass, &Velocity );
 
   // correct velocities (rather momenta) so that center of mass remains motionless
   Velocity.Scale(1./IonMass);
   ActualTemp = 0.;
-  ActOnAllAtoms ( &atom::CorrectVelocity, &ActualTemp, MDSteps, &Velocity );
+  ActOnAllAtoms ( &atom::CorrectVelocity, &ActualTemp, MDSteps+1, &Velocity );
   Thermostats(configuration, ActualTemp, Berendsen);
   MDSteps++;