Changeset 8bc524 for molecuilder/src/moleculelist.cpp

Timestamp:

Nov 3, 2009, 12:37:55 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

5f9f8b

Parents:

df0520

git-author:

Frederik Heber <heber@…> (11/03/09 08:41:45)

git-committer:

Frederik Heber <heber@…> (11/03/09 12:37:55)

Message:

Several memory bugfixes (thx valgrind).

• main() - shortened case switch after ParseCommandLineOptions()
• molecule::FragmentMolecule() - indentation around BondFragments fixed.
• LEAKFIX: main() - configuration was not destroyed in case switch.
• LEAKFIX: ~config() - BondGraph BG was not destroyed.
• LEAKFIX: ParseKeySetFile() - filename was not destroyed.
• LEAKFIX: molecule::FragmentMolecule() - BackEdgeStack (returned from DepthFirstSearchAnalysis()) was not destroyed.
• LEAKFIX: molecule::FragmentMolecule() - BondFragments was not destroyed.
• LEAKFIX: MemoryUsageObserver::~MemoryUsageObserver() -- frees all remaining unbfree'd memory
• BUGFIX: MoleculeListClass::OutputConfigForListOfFragments() - FragmentNumber was delete'd not Free'd
• BUGFIX: ParseCommandLineOptions() - Free() of ListOfLocalAtoms had FragmentCounter instead of i
• BUGFIX: ParseCommandLineOptions() had BackEdgeStack in case 'D' instead of LocalBackEdgeStack for the CycliCStructureAnalysis()
• BUGFIX: StackClass<T>::StackClass() did not initialize StackList to NULL (are pointers anyway).
• MolecularLeafWalker::FillBondStructureFromReference() - no more performs its actions recursively (just complicates things unnecessarily).
• ParseCommandLineOptions() and molecule::FragmentMolecule() adapted to MolecularLeafWalker::FillBondStructureFromReference() changes.
• DepthFirstSearchAnalysis_Init() now does all of the initialisation of DepthFirstSearchAnalysis() and get molecule instead of AtomCount and BondCount

Fixed Calloc:

• MemoryAllocatorTest::MallocTest() and MemoryAllocatorTest::CallocTest() perform test on array of 10 with writing to it (revealed Calloc() bug)
• LEAKFIX: MemoryAllocatorTest::tearDown() - instance was not free'd
• BUGFIX: Calloc() - calloc() is called with num and sizeof, not num and initial_value!
• FIX: Malloc() to Calloc(): CreateFatherLookupTable(), molecule::IsEqualToWithinThreshold(), molecule::ConstrainedPotential(), PrintPermutationMap(), FillDistanceList() (initialization not needed anymore due to Calloc(), molecule::MinimiseConstrainedPotential(), molecule::ParseOrderAtSiteFromFile(), StoreFragmentFromKeySet_Init() (initialization not needed anymore due to Calloc(), molecule::StoreFragmentFromKeySet(), molecule::PowerSetGenerator(), molecule::FragmentBOSSANOVA(), molecule::ScanForPeriodicCorrection(), molecule::CreateAdjacencyList(), InitializeBFSAccounting(), BreadthFirstSearchAdd_Init(), BuildInducedSubgraph_Init(), MoleculeListClass::AddHydrogenCorrection(), MoleculeLeafClass::FillListOfLocalAtoms(), MoleculeLeafClass::AssignKeySetsToFragment(), StackClass<T>::StackClass()

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

File:

• molecuilder/src/moleculelist.cpp (modified) (9 diffs)

molecuilder/src/moleculelist.cpp

@@ -422 +422 @@
 
   // 0b. allocate memory for constants
-  FitConstant = Malloc<double**>(3, "MoleculeListClass::AddHydrogenCorrection: ***FitConstant");
+  FitConstant = Calloc<double**>(3, "MoleculeListClass::AddHydrogenCorrection: ***FitConstant");
   for (int k = 0; k < 3; k++) {
-    FitConstant[k] = Malloc<double*>(a, "MoleculeListClass::AddHydrogenCorrection: **FitConstant[]");
+    FitConstant[k] = Calloc<double*>(a, "MoleculeListClass::AddHydrogenCorrection: **FitConstant[]");
     for (int i = a; i--;) {
-      FitConstant[k][i] = Malloc<double>(b, "MoleculeListClass::AddHydrogenCorrection: *FitConstant[][]");
+      FitConstant[k][i] = Calloc<double>(b, "MoleculeListClass::AddHydrogenCorrection: *FitConstant[][]");
     }
   }
@@ -471 +471 @@
 
   // 0d. allocate final correction matrix
-  correction = Malloc<double*>(a, "MoleculeListClass::AddHydrogenCorrection: **correction");
+  correction = Calloc<double*>(a, "MoleculeListClass::AddHydrogenCorrection: **correction");
   for (int i = a; i--;)
-    correction[i] = Malloc<double>(b, "MoleculeListClass::AddHydrogenCorrection: *correction[]");
+    correction[i] = Calloc<double>(b, "MoleculeListClass::AddHydrogenCorrection: *correction[]");
 
   // 1a. go through every molecule in the list
@@ -548 +548 @@
   output.close();
   // 6. free memory of parsed matrices
-  FitConstant = Malloc<double**>(a, "MoleculeListClass::AddHydrogenCorrection: ***FitConstant");
   for (int k = 0; k < 3; k++) {
-    FitConstant[k] = Malloc<double*>(a, "MoleculeListClass::AddHydrogenCorrection: **FitConstant[]");
     for (int i = a; i--;) {
-      FitConstant[k][i] = Malloc<double>(b, "MoleculeListClass::AddHydrogenCorrection: *FitConstant[][]");
-    }
-  }
+      Free(&FitConstant[k][i]);
+    }
+    Free(&FitConstant[k]);
+  }
+  Free(&FitConstant);
   cout << "done." << endl;
   return true;
@@ -712 +712 @@
     //outputFragment.close();
     //outputFragment.clear();
-    delete (FragmentNumber);
-    //Free(&FragmentNumber);
+    Free(&FragmentNumber);
   }
   cout << " done." << endl;
@@ -848 +847 @@
       }
     }
-    FragmentCounter++;
-    if (next != NULL)
-      status = next->FillBondStructureFromReference(out, reference, FragmentCounter, ListOfLocalAtoms);
-    FragmentCounter--;
+//    FragmentCounter++;
+//    if (next != NULL)
+//      status = next->FillBondStructureFromReference(out, reference, FragmentCounter, ListOfLocalAtoms);
+//    FragmentCounter--;
   }
 
@@ -860 +859 @@
       Free(&ListOfLocalAtoms);
   }
-  FragmentCounter--;
   *out << Verbose(1) << "End of FillBondStructureFromReference." << endl;
   return status;
@@ -907 +905 @@
 
 /** Fills a lookup list of father's Atom::nr -> atom for each subgraph.
- * \param *out output stream fro debugging
+ * \param *out output stream from debugging
  * \param ***ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
  * \param FragmentCounter counts the fragments as we move along the list
  * \param GlobalAtomCount number of atoms in the complete molecule
  * \param &FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
- * \return true - succes, false - failure
+ * \return true - success, false - failure
  */
 bool MoleculeLeafClass::FillListOfLocalAtoms(ofstream *out, atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList)
@@ -921 +919 @@
   if (ListOfLocalAtoms == NULL) { // allocated initial pointer
     // allocate and set each field to NULL
-    ListOfLocalAtoms = Malloc<atom**>(Counter, "MoleculeLeafClass::FillBondStructureFromReference - ***ListOfLocalAtoms");
+    ListOfLocalAtoms = Calloc<atom**>(Counter, "MoleculeLeafClass::FillListOfLocalAtoms - ***ListOfLocalAtoms");
     if (ListOfLocalAtoms != NULL) {
-      for (int i = Counter; i--;)
-        ListOfLocalAtoms[i] = NULL;
       FreeList = FreeList && true;
     } else
@@ -965 +961 @@
   if (FragmentList == NULL) {
     KeySetCounter = Count();
-    FragmentList = Malloc<Graph*>(KeySetCounter, "MoleculeLeafClass::AssignKeySetsToFragment - **FragmentList");
-    for (int i = KeySetCounter; i--;)
-      FragmentList[i] = NULL;
+    FragmentList = Calloc<Graph*>(KeySetCounter, "MoleculeLeafClass::AssignKeySetsToFragment - **FragmentList");
     KeySetCounter = 0;
   }