Changeset 920c70 for src/molecule.cpp

Timestamp:

May 31, 2010, 1:09:58 PM (15 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, 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.cpp (modified) (6 diffs)

src/molecule.cpp

@@ -242 +242 @@
     Orthovector1.MatrixMultiplication(matrix);
     InBondvector -= Orthovector1; // subtract just the additional translation
-    Free(&matrix);
+    delete[](matrix);
     bondlength = InBondvector.Norm();
 //    Log() << Verbose(4) << "Corrected InBondvector is now: ";
@@ -251 +251 @@
   InBondvector.Normalize();
   // get typical bond length and store as scale factor for later
+  ASSERT(TopOrigin->type != NULL, "AddHydrogenReplacementAtom: element of TopOrigin is not given.");
   BondRescale = TopOrigin->type->HBondDistance[TopBond->BondDegree-1];
   if (BondRescale == -1) {
@@ -472 +473 @@
       break;
   }
-  Free(&matrix);
+  delete[](matrix);
 
 //  Log() << Verbose(3) << "End of AddHydrogenReplacementAtom." << endl;
@@ -1034 +1035 @@
   if (result) {
     DoLog(5) && (Log() << Verbose(5) << "Calculating distances" << endl);
-    Distances = Calloc<double>(AtomCount, "molecule::IsEqualToWithinThreshold: Distances");
-    OtherDistances = Calloc<double>(AtomCount, "molecule::IsEqualToWithinThreshold: OtherDistances");
+    Distances = new double[AtomCount];
+    OtherDistances = new double[AtomCount];
     SetIndexedArrayForEachAtomTo ( Distances, &atom::nr, &atom::DistanceSquaredToVector, (const Vector &)CenterOfGravity);
     SetIndexedArrayForEachAtomTo ( OtherDistances, &atom::nr, &atom::DistanceSquaredToVector, (const Vector &)CenterOfGravity);
+    for(int i=0;i<AtomCount;i++) {
+      Distances[i] = 0.;
+      OtherDistances[i] = 0.;
+    }
 
     /// ... sort each list (using heapsort (o(N log N)) from GSL)
     DoLog(5) && (Log() << Verbose(5) << "Sorting distances" << endl);
-    PermMap = Calloc<size_t>(AtomCount, "molecule::IsEqualToWithinThreshold: *PermMap");
-    OtherPermMap = Calloc<size_t>(AtomCount, "molecule::IsEqualToWithinThreshold: *OtherPermMap");
+    PermMap = new size_t[AtomCount];
+    OtherPermMap = new size_t[AtomCount];
+    for(int i=0;i<AtomCount;i++) {
+      PermMap[i] = 0;
+      OtherPermMap[i] = 0;
+    }
     gsl_heapsort_index (PermMap, Distances, AtomCount, sizeof(double), CompareDoubles);
     gsl_heapsort_index (OtherPermMap, OtherDistances, AtomCount, sizeof(double), CompareDoubles);
-    PermutationMap = Calloc<int>(AtomCount, "molecule::IsEqualToWithinThreshold: *PermutationMap");
+    PermutationMap = new int[AtomCount];
+    for(int i=0;i<AtomCount;i++)
+      PermutationMap[i] = 0;
     DoLog(5) && (Log() << Verbose(5) << "Combining Permutation Maps" << endl);
     for(int i=AtomCount;i--;)
@@ -1060 +1071 @@
 
     // free memory
-    Free(&PermMap);
-    Free(&OtherPermMap);
-    Free(&Distances);
-    Free(&OtherDistances);
+    delete[](PermMap);
+    delete[](OtherPermMap);
+    delete[](Distances);
+    delete[](OtherDistances);
     if (flag) { // if not equal
-      Free(&PermutationMap);
+      delete[](PermutationMap);
       result = false;
     }
@@ -1091 +1102 @@
   atom *Walker = NULL, *OtherWalker = NULL;
   DoLog(3) && (Log() << Verbose(3) << "Begin of GetFatherAtomicMap." << endl);
-  int *AtomicMap = Malloc<int>(AtomCount, "molecule::GetAtomicMap: *AtomicMap");
+  int *AtomicMap = new int[AtomCount];
   for (int i=AtomCount;i--;)
     AtomicMap[i] = -1;