Changeset 7218f8 for src/molecule_fragmentation.cpp

Timestamp:

Nov 3, 2009, 12:37:55 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:

2aeefd

Parents:

fa649a

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:

• src/molecule_fragmentation.cpp (modified) (14 diffs)

src/molecule_fragmentation.cpp

@@ -123 +123 @@
   }
 
+  Free(&filename);
   return status;
 };
@@ -574 +575 @@
   // ===== 2. perform a DFS analysis to gather info on cyclic structure and a list of disconnected subgraphs =====
   Subgraphs = DepthFirstSearchAnalysis(out, BackEdgeStack);
-  // fill the bond structure of the individually stored subgraphs
-  Subgraphs->next->FillBondStructureFromReference(out, this, (FragmentCounter = 0), ListOfLocalAtoms, false);  // we want to keep the created ListOfLocalAtoms
+
   // analysis of the cycles (print rings, get minimum cycle length) for each subgraph
   for(int i=AtomCount;i--;)
@@ -583 +583 @@
   while (MolecularWalker->next != NULL) {
     MolecularWalker = MolecularWalker->next;
+    // fill the bond structure of the individually stored subgraphs
+  MolecularWalker->FillBondStructureFromReference(out, this, FragmentCounter, ListOfLocalAtoms, false);  // we want to keep the created ListOfLocalAtoms
     *out << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
     LocalBackEdgeStack = new StackClass<bond *> (MolecularWalker->Leaf->BondCount);
@@ -599 +601 @@
     delete(LocalBackEdgeStack);
   }
+  delete(BackEdgeStack);
 
   // ===== 3. if structure still valid, parse key set file and others =====
@@ -663 +666 @@
   // ===== 8b. gather keyset lists (graphs) from all subgraphs and transform into MoleculeListClass =====
   //if (FragmentationToDo) {    // we should always store the fragments again as coordination might have changed slightly without changing bond structure
-    // allocate memory for the pointer array and transmorph graphs into full molecular fragments
-    BondFragments = new MoleculeListClass();
-    int k=0;
-    for(Graph::iterator runner = TotalGraph.begin(); runner != TotalGraph.end(); runner++) {
-      KeySet test = (*runner).first;
-      *out << "Fragment No." << (*runner).second.first << " with TEFactor " << (*runner).second.second << "." << endl;
-      BondFragments->insert(StoreFragmentFromKeySet(out, test, configuration));
-      k++;
-    }
-    *out << k << "/" << BondFragments->ListOfMolecules.size() << " fragments generated from the keysets." << endl;
-
-    // ===== 9. Save fragments' configuration and keyset files et al to disk ===
-    if (BondFragments->ListOfMolecules.size() != 0) {
-      // create the SortIndex from BFS labels to order in the config file
-      CreateMappingLabelsToConfigSequence(out, SortIndex);
-
-      *out << Verbose(1) << "Writing " << BondFragments->ListOfMolecules.size() << " possible bond fragmentation configs" << endl;
-      if (BondFragments->OutputConfigForListOfFragments(out, configuration, SortIndex))
-        *out << Verbose(1) << "All configs written." << endl;
-      else
-        *out << Verbose(1) << "Some config writing failed." << endl;
-
-      // store force index reference file
-      BondFragments->StoreForcesFile(out, configuration->configpath, SortIndex);
-
-      // store keysets file
-      StoreKeySetFile(out, TotalGraph, configuration->configpath);
-
-      // store Adjacency file
-      StoreAdjacencyToFile(out, configuration->configpath);
-
-      // store Hydrogen saturation correction file
-      BondFragments->AddHydrogenCorrection(out, configuration->configpath);
-
-      // store adaptive orders into file
-      StoreOrderAtSiteFile(out, configuration->configpath);
-
-      // restore orbital and Stop values
-      CalculateOrbitals(*configuration);
-
-      // free memory for bond part
-      *out << Verbose(1) << "Freeing bond memory" << endl;
-      delete(FragmentList); // remove bond molecule from memory
-      Free(&SortIndex);
-    } else
-      *out << Verbose(1) << "FragmentList is zero on return, splitting failed." << endl;
-  //} else
-  //  *out << Verbose(1) << "No fragments to store." << endl;
+  // allocate memory for the pointer array and transmorph graphs into full molecular fragments
+  BondFragments = new MoleculeListClass();
+  int k=0;
+  for(Graph::iterator runner = TotalGraph.begin(); runner != TotalGraph.end(); runner++) {
+    KeySet test = (*runner).first;
+    *out << "Fragment No." << (*runner).second.first << " with TEFactor " << (*runner).second.second << "." << endl;
+    BondFragments->insert(StoreFragmentFromKeySet(out, test, configuration));
+    k++;
+  }
+  *out << k << "/" << BondFragments->ListOfMolecules.size() << " fragments generated from the keysets." << endl;
+
+  // ===== 9. Save fragments' configuration and keyset files et al to disk ===
+  if (BondFragments->ListOfMolecules.size() != 0) {
+    // create the SortIndex from BFS labels to order in the config file
+    CreateMappingLabelsToConfigSequence(out, SortIndex);
+
+    *out << Verbose(1) << "Writing " << BondFragments->ListOfMolecules.size() << " possible bond fragmentation configs" << endl;
+    if (BondFragments->OutputConfigForListOfFragments(out, configuration, SortIndex))
+      *out << Verbose(1) << "All configs written." << endl;
+    else
+      *out << Verbose(1) << "Some config writing failed." << endl;
+
+    // store force index reference file
+    BondFragments->StoreForcesFile(out, configuration->configpath, SortIndex);
+
+    // store keysets file
+    StoreKeySetFile(out, TotalGraph, configuration->configpath);
+
+    // store Adjacency file
+    StoreAdjacencyToFile(out, configuration->configpath);
+
+    // store Hydrogen saturation correction file
+    BondFragments->AddHydrogenCorrection(out, configuration->configpath);
+
+    // store adaptive orders into file
+    StoreOrderAtSiteFile(out, configuration->configpath);
+
+    // restore orbital and Stop values
+    CalculateOrbitals(*configuration);
+
+    // free memory for bond part
+    *out << Verbose(1) << "Freeing bond memory" << endl;
+    delete(FragmentList); // remove bond molecule from memory
+    Free(&SortIndex);
+  } else {
+    *out << Verbose(1) << "FragmentList is zero on return, splitting failed." << endl;
+  }
+  delete(BondFragments);
   *out << Verbose(0) << "End of bond fragmentation." << endl;
 
@@ -751 +754 @@
 bool molecule::ParseOrderAtSiteFromFile(ofstream *out, char *path)
 {
-  unsigned char *OrderArray = Malloc<unsigned char>(AtomCount, "molecule::ParseOrderAtSiteFromFile - *OrderArray");
-  bool *MaxArray = Malloc<bool>(AtomCount, "molecule::ParseOrderAtSiteFromFile - *MaxArray");
+  unsigned char *OrderArray = Calloc<unsigned char>(AtomCount, "molecule::ParseOrderAtSiteFromFile - *OrderArray");
+  bool *MaxArray = Calloc<bool>(AtomCount, "molecule::ParseOrderAtSiteFromFile - *MaxArray");
   bool status;
   int AtomNr, value;
@@ -759 +762 @@
 
   *out << Verbose(1) << "Begin of ParseOrderAtSiteFromFile" << endl;
-  for(int i=AtomCount;i--;)
-    OrderArray[i] = 0;
   line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
   file.open(line.str().c_str());
   if (file != NULL) {
-    for (int i=AtomCount;i--;) { // initialise with 0
-      OrderArray[i] = 0;
-      MaxArray[i] = 0;
-    }
     while (!file.eof()) { // parse from file
       AtomNr = -1;
@@ -830 +827 @@
  * \param *Leaf fragment molecule
  * \param &Leaflet pointer to KeySet structure
- * \param **SonList list which atom of \a *Leaf is a son of which atom in \a *mol
+ * \param **SonList calloc'd list which atom of \a *Leaf is a son of which atom in \a *mol
  * \return number of atoms in fragment
  */
@@ -840 +837 @@
   for(int i=NDIM*2;i--;)
     Leaf->cell_size[i] = mol->cell_size[i];
-
-  // initialise SonList (indicates when we need to replace a bond with hydrogen instead)
-  for(int i=mol->AtomCount;i--;)
-    SonList[i] = NULL;
 
   // first create the minimal set of atoms from the KeySet
@@ -924 +917 @@
 molecule * molecule::StoreFragmentFromKeySet(ofstream *out, KeySet &Leaflet, bool IsAngstroem)
 {
-  atom **SonList = Malloc<atom*>(AtomCount, "molecule::StoreFragmentFromStack: **SonList");
+  atom **SonList = Calloc<atom*>(AtomCount, "molecule::StoreFragmentFromStack: **SonList");
   molecule *Leaf = new molecule(elemente);
 
@@ -1389 +1382 @@
 
     // prepare the subset and call the generator
-    BondsList = Malloc<bond*>(FragmentSearch.BondsPerSPCount[0], "molecule::PowerSetGenerator: **BondsList");
+    BondsList = Calloc<bond*>(FragmentSearch.BondsPerSPCount[0], "molecule::PowerSetGenerator: **BondsList");
     BondsList[0] = FragmentSearch.BondsPerSPList[0]->next;  // on SP level 0 there's only the root bond
 
@@ -1544 +1537 @@
   // FragmentLowerOrdersList is a 2D-array of pointer to MoleculeListClass objects, one dimension represents the ANOVA expansion of a single order (i.e. 5)
   // with all needed lower orders that are subtracted, the other dimension is the BondOrder (i.e. from 1 to 5)
-  NumMoleculesOfOrder = Malloc<int>(UpgradeCount, "molecule::FragmentBOSSANOVA: *NumMoleculesOfOrder");
-  FragmentLowerOrdersList = Malloc<Graph**>(UpgradeCount, "molecule::FragmentBOSSANOVA: ***FragmentLowerOrdersList");
+  NumMoleculesOfOrder = Calloc<int>(UpgradeCount, "molecule::FragmentBOSSANOVA: *NumMoleculesOfOrder");
+  FragmentLowerOrdersList = Calloc<Graph**>(UpgradeCount, "molecule::FragmentBOSSANOVA: ***FragmentLowerOrdersList");
 
   // initialise the fragments structure
-  FragmentSearch.ShortestPathList = Malloc<int>(AtomCount, "molecule::PowerSetGenerator: *ShortestPathList");
   FragmentSearch.FragmentCounter = 0;
   FragmentSearch.FragmentSet = new KeySet;
   FragmentSearch.Root = FindAtom(RootKeyNr);
+  FragmentSearch.ShortestPathList = Malloc<int>(AtomCount, "molecule::PowerSetGenerator: *ShortestPathList");
   for (int i=AtomCount;i--;) {
     FragmentSearch.ShortestPathList[i] = -1;
@@ -1587 +1580 @@
       // allocate memory for all lower level orders in this 1D-array of ptrs
       NumLevels = 1 << (Order-1); // (int)pow(2,Order);
-      FragmentLowerOrdersList[RootNr] = Malloc<Graph*>(NumLevels, "molecule::FragmentBOSSANOVA: **FragmentLowerOrdersList[]");
-      for (int i=0;i<NumLevels;i++)
-        FragmentLowerOrdersList[RootNr][i] = NULL;
+      FragmentLowerOrdersList[RootNr] = Calloc<Graph*>(NumLevels, "molecule::FragmentBOSSANOVA: **FragmentLowerOrdersList[]");
 
       // create top order where nothing is reduced
@@ -1665 +1656 @@
   *out << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl;
 
-  ColorList = Malloc<enum Shading>(AtomCount, "molecule::ScanForPeriodicCorrection: *ColorList");
+  ColorList = Calloc<enum Shading>(AtomCount, "molecule::ScanForPeriodicCorrection: *ColorList");
   while (flag) {
     // remove bonds that are beyond bonddistance