Changeset 7218f8 for src/molecule_dynamics.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, Candidate_v1.7.1, 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:

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_dynamics.cpp (modified) (3 diffs)

src/molecule_dynamics.cpp

@@ -193 +193 @@
 {
   stringstream zeile1, zeile2;
-  int *DoubleList = Malloc<int>(AtomCount, "PrintPermutationMap: *DoubleList");
+  int *DoubleList = Calloc<int>(AtomCount, "PrintPermutationMap: *DoubleList");
   int doubles = 0;
-  for (int i=0;i<AtomCount;i++)
-    DoubleList[i] = 0;
   zeile1 << "PermutationMap: ";
   zeile2 << "                ";
@@ -243 +241 @@
 void CreateInitialLists(ofstream *out, molecule *mol, struct EvaluatePotential &Params)
 {
-  for (int i=mol->AtomCount; i--;)
-    Params.DoubleList[i] = 0;  // stores for how many atoms in startstep this atom is a target in endstep
-
   atom *Walker = mol->start;
   while (Walker->next != mol->end) {
@@ -347 +342 @@
   double Potential, OldPotential, OlderPotential;
   struct EvaluatePotential Params;
-  Params.PermutationMap = Malloc<atom*>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.**PermutationMap");
+  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 = Malloc<int>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.*DoubleList");
+  Params.DoubleList = Calloc<int>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.*DoubleList");
   Params.StepList = Malloc<DistanceMap::iterator>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.*StepList");
   int round;