Changeset 920c70 for src/molecule_dynamics.cpp

Timestamp:

May 31, 2010, 1:09:58 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, Candidate_v1.7.0, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

42af9e

Parents:

87b597

Message:

Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and delete/delete[].

Due to the new MemDebug framework there is no need (or even unnecessary/unwanted competition between it and) for the MemoryAllocator and ..UsageObserver anymore.
They can however still be used with c codes such as pcp and alikes.

In Molecuilder lots of glibc corruptions arose and the C-like syntax make it generally harder to get allocation and deallocation straight.

Signed-off-by: Frederik Heber <heber@…>

File:

• src/molecule_dynamics.cpp (modified) (8 diffs)

src/molecule_dynamics.cpp

@@ -190 +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: ";
@@ -204 +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;
 };
@@ -339 +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
@@ -363 +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
@@ -445 +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);
 };
@@ -488 +496 @@
     MinimiseConstrainedPotential(PermutationMap, startstep, endstep, configuration.GetIsAngstroem());
   else {
-    PermutationMap = Malloc<atom *>(AtomCount, "molecule::LinearInterpolationBetweenConfiguration: **PermutationMap");
+    PermutationMap = new atom *[AtomCount];
     SetIndexedArrayForEachAtomTo( PermutationMap, &atom::nr );
   }
@@ -523 +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;
@@ -590 +599 @@
       ConstrainedPotentialEnergy = MinimiseConstrainedPotential(PermutationMap,configuration.DoConstrainedMD, 0, configuration.GetIsAngstroem());
       EvaluateConstrainedForces(configuration.DoConstrainedMD, 0, PermutationMap, &Force);
-      Free(&PermutationMap);
+      delete[](PermutationMap);
     }