Changeset 8e0c63 for src

Timestamp:

Jun 29, 2010, 3:37:58 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:

56fb09, bdc91e

Parents:

ef7d30

git-author:

Frederik Heber <heber@…> (06/29/10 15:25:53)

git-committer:

Frederik Heber <heber@…> (06/29/10 15:37:58)

Message:

MEMFIX: MatrixContainer::MatrixContainer() made some initial allocations that were simply overwritten afterwards and not free'd.

• This probably originates from the removal of Malloc/Free.
• TESTFIX: Molecules/5 now returns 0 and not 134 anymore. (but still BROKEN as it seems)

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

File:

• src/parser.cpp (modified) (7 diffs)

src/parser.cpp

@@ -76 +76 @@
 MatrixContainer::~MatrixContainer() {
   if (Matrix != NULL) {
+    // free Matrix[MatrixCounter]
+    if ((ColumnCounter != NULL) && (RowCounter != NULL) && (Matrix[MatrixCounter] != NULL))
+      for(int j=RowCounter[MatrixCounter]+1;j--;)
+        delete[](Matrix[MatrixCounter][j]);
+    //if (MatrixCounter != 0)
+    delete[](Matrix[MatrixCounter]);
+    // free all matrices but ultimate one
     for(int i=MatrixCounter;i--;) {
       if ((ColumnCounter != NULL) && (RowCounter != NULL)) {
@@ -83 +90 @@
       }
     }
-    if ((ColumnCounter != NULL) && (RowCounter != NULL) && (Matrix[MatrixCounter] != NULL))
-      for(int j=RowCounter[MatrixCounter]+1;j--;)
-        delete[](Matrix[MatrixCounter][j]);
-    if (MatrixCounter != 0)
-      delete[](Matrix[MatrixCounter]);
     delete[](Matrix);
   }
+  // free indices
   if (Indices != NULL)
     for(int i=MatrixCounter+1;i--;) {
@@ -96 +99 @@
   delete[](Indices);
   
+  // free header and counters
   if (Header != NULL)
     for(int i=MatrixCounter+1;i--;)
@@ -168 +172 @@
 
   // parse header
+  if (Header[MatrixNr] != NULL)
+    delete[] Header[MatrixNr];
   Header[MatrixNr] = new char[1024];
   for (int m=skiplines+1;m--;)
@@ -207 +213 @@
   // allocate matrix if it's not zero dimension in one direction
   if ((ColumnCounter[MatrixNr] > 0) && (RowCounter[MatrixNr] > -1)) {
+    if (Matrix[MatrixNr] != NULL)
+      delete[] Matrix[MatrixNr];
     Matrix[MatrixNr] = new double*[RowCounter[MatrixNr] + 1];
-  
+    for(int j=0;j<RowCounter[MatrixNr]+1;j++)
+      Matrix[MatrixNr][j] = 0;
+
     // parse in each entry for this matrix
     input.clear();
@@ -219 +229 @@
     strncpy(Header[MatrixNr], line.str().c_str(), 1023);  
     for(int j=0;j<RowCounter[MatrixNr];j++) {
+      if (Matrix[MatrixNr][j] != NULL)
+        delete[] Matrix[MatrixNr][j];
       Matrix[MatrixNr][j] = new double[ColumnCounter[MatrixNr]];
+      for(int k=0;k<ColumnCounter[MatrixNr];k++)
+        Matrix[MatrixNr][j][k] = 0;
+
       input.getline(filename, 1023);
       stringstream lines(filename);
@@ -229 +244 @@
         //Log() << Verbose(1) << " " << setprecision(2) << Matrix[MatrixNr][j][k] << endl;
       }
+      if (Matrix[MatrixNr][ RowCounter[MatrixNr] ] != NULL)
+        delete[] Matrix[MatrixNr][ RowCounter[MatrixNr] ];
       Matrix[MatrixNr][ RowCounter[MatrixNr] ] = new double[ColumnCounter[MatrixNr]];
       for(int j=ColumnCounter[MatrixNr];j--;)