Changeset 920c70 for src/molecule_graph.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_graph.cpp (modified) (15 diffs)

src/molecule_graph.cpp

@@ -143 +143 @@
     // create a list to map Tesselpoint::nr to atom *
     DoLog(2) && (Log() << Verbose(2) << "Creating TesselPoint to atom map ... " << endl);
-    AtomMap = Calloc<atom *> (AtomCount, "molecule::CreateAdjacencyList - **AtomCount");
+    AtomMap = new atom *[AtomCount];
+    for (int i=0;i<AtomCount;i++)
+      AtomMap[i] = NULL;
     Walker = start;
     while (Walker->next != end) {
@@ -194 +196 @@
           }
         }
-    Free(&AtomMap);
+    delete[](AtomMap);
     delete (LC);
     DoLog(1) && (Log() << Verbose(1) << "I detected " << BondCount << " bonds in the molecule with distance " << BondDistance << "." << endl);
@@ -630 +632 @@
 {
   BFS.AtomCount = AtomCount;
-  BFS.PredecessorList = Calloc<atom*> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: **PredecessorList");
-  BFS.ShortestPathList = Malloc<int> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ShortestPathList");
-  BFS.ColorList = Calloc<enum Shading> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ColorList");
+  BFS.PredecessorList = new atom*[AtomCount];
+  BFS.ShortestPathList = new int[AtomCount];
+  BFS.ColorList = new enum Shading[AtomCount];
   BFS.BFSStack = new StackClass<atom *> (AtomCount);
 
-  for (int i = AtomCount; i--;)
+  for (int i = AtomCount; i--;) {
     BFS.ShortestPathList[i] = -1;
+    BFS.PredecessorList[i] = 0;
+  }
 };
 
@@ -645 +649 @@
 void FinalizeBFSAccounting(struct BFSAccounting &BFS)
 {
-  Free(&BFS.PredecessorList);
-  Free(&BFS.ShortestPathList);
-  Free(&BFS.ColorList);
+  delete[](BFS.PredecessorList);
+  delete[](BFS.ShortestPathList);
+  delete[](BFS.ColorList);
   delete (BFS.BFSStack);
   BFS.AtomCount = 0;
@@ -1067 +1071 @@
 
   // allocate storage structure
-  CurrentBonds = Calloc<int> (8, "molecule::CheckAdjacencyFileAgainstMolecule - CurrentBonds"); // contains parsed bonds of current atom
+  CurrentBonds = new int[8]; // contains parsed bonds of current atom
+  for(int i=0;i<8;i++)
+    CurrentBonds[i] = 0;
   return true;
 }
@@ -1076 +1082 @@
   File.close();
   File.clear();
-  Free(&CurrentBonds);
+  delete[](CurrentBonds);
 }
 ;
@@ -1120 +1126 @@
   bool status = true;
   atom *Walker = NULL;
-  char *buffer = NULL;
   int *CurrentBonds = NULL;
   int NonMatchNumber = 0; // will number of atoms with differing bond structure
@@ -1130 +1135 @@
   }
 
-  buffer = Malloc<char> (MAXSTRINGSIZE, "molecule::CheckAdjacencyFileAgainstMolecule: *buffer");
+  char buffer[MAXSTRINGSIZE];
   // Parse the file line by line and count the bonds
   while (!File.eof()) {
@@ -1148 +1153 @@
     }
   }
-  Free(&buffer);
   CheckAdjacencyFileAgainstMolecule_Finalize(File, CurrentBonds);
 
@@ -1202 +1206 @@
   BFS.AtomCount = AtomCount;
   BFS.BondOrder = BondOrder;
-  BFS.PredecessorList = Calloc<atom*> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: **PredecessorList");
-  BFS.ShortestPathList = Calloc<int> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ShortestPathList");
-  BFS.ColorList = Malloc<enum Shading> (AtomCount, "molecule::BreadthFirstSearchAdd_Init: *ColorList");
+  BFS.PredecessorList = new atom*[AtomCount];
+  BFS.ShortestPathList = new int[AtomCount];
+  BFS.ColorList = new enum Shading[AtomCount];
   BFS.BFSStack = new StackClass<atom *> (AtomCount);
 
@@ -1213 +1217 @@
   // initialise each vertex as white with no predecessor, empty queue, color Root lightgray
   for (int i = AtomCount; i--;) {
+    BFS.PredecessorList[i] = NULL;
     BFS.ShortestPathList[i] = -1;
     if ((AddedAtomList != NULL) && (AddedAtomList[i] != NULL)) // mark already present atoms (i.e. Root and maybe others) as visited
@@ -1219 +1224 @@
       BFS.ColorList[i] = white;
   }
-  //BFS.ShortestPathList[Root->nr] = 0; //is set due to Calloc()
+  //BFS.ShortestPathList[Root->nr] = 0; // done by Calloc
 }
 ;
@@ -1225 +1230 @@
 void BreadthFirstSearchAdd_Free(struct BFSAccounting &BFS)
 {
-  Free(&BFS.PredecessorList);
-  Free(&BFS.ShortestPathList);
-  Free(&BFS.ColorList);
+  delete[](BFS.PredecessorList);
+  delete[](BFS.ShortestPathList);
+  delete[](BFS.ColorList);
   delete (BFS.BFSStack);
   BFS.AtomCount = 0;
@@ -1366 +1371 @@
 {
   // reset parent list
-  ParentList = Calloc<atom*> (AtomCount, "molecule::BuildInducedSubgraph_Init: **ParentList");
+  ParentList = new atom*[AtomCount];
+  for (int i=0;i<AtomCount;i++)
+    ParentList[i] = NULL;
   DoLog(3) && (Log() << Verbose(3) << "Resetting ParentList." << endl);
 }
@@ -1388 +1395 @@
 void BuildInducedSubgraph_Finalize(atom **&ParentList)
 {
-  Free(&ParentList);
+  delete[](ParentList);
 }
 ;