Changeset f2bb0f

Timestamp:

Mar 18, 2010, 3:32:00 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

53731f

Parents:

75ac0c

Message:

FIX: Repaired memory smashing in CreateAdjacencyList

BROKEN: Unittests still fail

Location:

src

Files:

• Legacy/oldmenu.cpp (modified) (1 diff)
• Patterns/ObservedIterator.hpp (modified) (1 diff)
• World.cpp (modified) (1 diff)
• memoryallocator.hpp (modified) (2 diffs)
• molecule_graph.cpp (modified) (6 diffs)

src/Legacy/oldmenu.cpp

@@ -424 +424 @@
 void oldmenu::RemoveAtoms(molecule *mol)
 {
-  atom *first, *second;
+  atom *second;
   int axis;
   double tmp1, tmp2;

src/Patterns/ObservedIterator.hpp

@@ -70 +70 @@
   {
     ++iter;
+    return *this;
   }
 
-  ObservedIterator  operator++(int) // postfix with the dummy int parameter
+  ObservedIterator operator++(int) // postfix with the dummy int parameter
   {
     ObservedIterator ret(*this);

src/World.cpp

@@ -170 +170 @@
     atomId_t id = *(atomIdPool.begin());
     atomIdPool.erase(id);
+    return id;
   }
 }

src/memoryallocator.hpp

@@ -115 +115 @@
 template <typename X> void Free(X** buffer, const char *msg = NULL)
 {
-  std::cout << "!!!!!!!!!!!!!!!!!removing pointer to buffer !!!!!!!!!!!!" << std::endl;
   if ((buffer == NULL) || (*buffer == NULL))
     return;
@@ -131 +130 @@
 template <typename X> void Free(X* const buffer, const char *msg = NULL)
 {
-  std::cout << "!!!!!!!!!!!!!!!!!removing direct buffer !!!!!!!!!!!!" << std::endl;
   if ((buffer == NULL))
     return;

src/molecule_graph.cpp

@@ -17 +17 @@
 #include "memoryallocator.hpp"
 #include "molecule.hpp"
+#include "Helpers/Assert.hpp"
 
 struct BFSAccounting
@@ -101 +102 @@
   atom *Walker = NULL;
   atom *OtherWalker = NULL;
-  atom **AtomMap = NULL;
+  vector<atom*> AtomMap;
   int n[NDIM];
   double MinDistance, MaxDistance;
@@ -134 +135 @@
     // create a list to map Tesselpoint::nr to atom *
     Log() << Verbose(2) << "Creating TesselPoint to atom map ... " << endl;
-    AtomMap = Calloc<atom *> (AtomCount, "molecule::CreateAdjacencyList - **AtomCount");
-    for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
-      std::cout << "!!!!!!!!!!!!Copying pointer to Atom number: " << (*iter)->nr << std::endl;
-      AtomMap[(*iter)->nr] = (*iter);
-    }
+    //AtomMap = Calloc<atom *> (AtomCount, "molecule::CreateAdjacencyList - **AtomCount");
+    //for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+    //  std::cout << "!!!!!!!!!!!!Copying pointer to Atom number: " << (*iter)->nr << std::endl;
+    //  AtomMap[(*iter)->nr] = (*iter);
+    //}
+
+    copy(atoms.begin(),atoms.end(),back_inserter(AtomMap));
 
     // 3a. go through every cell
@@ -149 +152 @@
           if (List != NULL) {
             for (LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
-              Walker = AtomMap[(*Runner)->nr];
+              //Walker = AtomMap[(*Runner)->nr];
+              Walker = dynamic_cast<atom*>(*Runner);
+              ASSERT(Walker,"Tesselpoint that was not an atom retrieved from LinkedNode");
               //Log() << Verbose(0) << "Current Atom is " << *Walker << "." << endl;
               // 3c. check for possible bond between each atom in this and every one in the 27 cells
@@ -160 +165 @@
                       for (LinkedNodes::const_iterator OtherRunner = OtherList->begin(); OtherRunner != OtherList->end(); OtherRunner++) {
                         if ((*OtherRunner)->nr > Walker->nr) {
-                          OtherWalker = AtomMap[(*OtherRunner)->nr];
+                          //OtherWalker = AtomMap[(*OtherRunner)->nr];
+                          OtherWalker = dynamic_cast<atom*>(*OtherRunner);
+                          ASSERT(OtherWalker,"TesselPoint that was not an atom retrieved from LinkedNode");
                           //Log() << Verbose(1) << "Checking distance " << OtherWalker->x.PeriodicDistanceSquared(&(Walker->x), cell_size) << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
                           (BG->*minmaxdistance)(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
@@ -178 +185 @@
           }
         }
-    std::cout << "trying to remove Pointer to buffer " << std::endl;
-    Free(&AtomMap);
     delete (LC);
     Log() << Verbose(1) << "I detected " << BondCount << " bonds in the molecule with distance " << BondDistance << "." << endl;