Changeset 3c4b08

Timestamp:

May 5, 2008, 4:54:44 PM (17 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:

63382d

Parents:

2459b1

Message:

joiner crashed due to incorrect destructing of MatrixContainer, analyzer did not initialise KeySets in ParseKeySets

joiner crashed as ParseMatrix would return without free'ing initialized Matrix and RowCounter when suffix file cannot be opened. Now, they are initialized in such a manner that ~MatrixContainer recognizes and free's them
analyzer would stumble afgter parsing keysets on the order, as he was looking for -1 to which KeySets was not properly initialized but what should be read from KeySets file.
Also, analyzer would parse the final tab as a number which rendered nonsense. Hence, StoreKeySetFile does not ptroduce a tab after last entry per line anymore

File:

• src/parser.cpp (modified) (5 diffs)

src/parser.cpp

@@ -63 +63 @@
  */
 MatrixContainer::~MatrixContainer() {
-  if (Matrix != NULL)
+  if (Matrix != NULL) {
     for(int i=0;i<MatrixCounter;i++) {
-      if (RowCounter != NULL)
-        for(int j=0;j<=RowCounter[i];j++)
-          Free((void **)&Matrix[i][j], "MatrixContainer::~MatrixContainer: *Matrix[][]");
-      Free((void **)&Matrix[i], "MatrixContainer::~MatrixContainer: **Matrix[]");
-    }
-  if ((RowCounter != NULL) && (Matrix[MatrixCounter] != NULL))
-    for(int j=0;j<=RowCounter[MatrixCounter];j++)
-      Free((void **)&Matrix[MatrixCounter][j], "MatrixContainer::~MatrixContainer: *Matrix[MatrixCounter][]");
-  if (MatrixCounter != 0)
-    Free((void **)&Matrix[MatrixCounter], "MatrixContainer::~MatrixContainer: **Matrix[MatrixCounter]");
-  Free((void **)&Matrix, "MatrixContainer::~MatrixContainer: ***Matrix");
-  
+      if (RowCounter != NULL) {
+          for(int j=0;j<=RowCounter[i];j++)
+            Free((void **)&Matrix[i][j], "MatrixContainer::~MatrixContainer: *Matrix[][]");
+        Free((void **)&Matrix[i], "MatrixContainer::~MatrixContainer: **Matrix[]");
+      }
+    }
+    if ((RowCounter != NULL) && (Matrix[MatrixCounter] != NULL))
+      for(int j=0;j<=RowCounter[MatrixCounter];j++)
+        Free((void **)&Matrix[MatrixCounter][j], "MatrixContainer::~MatrixContainer: *Matrix[MatrixCounter][]");
+    if (MatrixCounter != 0)
+      Free((void **)&Matrix[MatrixCounter], "MatrixContainer::~MatrixContainer: **Matrix[MatrixCounter]");
+    Free((void **)&Matrix, "MatrixContainer::~MatrixContainer: ***Matrix");
+  }
   if (Indices != NULL)
     for(int i=0;i<=MatrixCounter;i++) {
@@ -101 +102 @@
   char *FragmentNumber = NULL;
   stringstream line;
-  double tmp;  
   
   Header = (char *) Malloc(sizeof(char)*1023, "MatrixContainer::ParseMatrix: *EnergyHeader");
@@ -123 +123 @@
   Matrix = (double ***) Malloc(sizeof(double **)*(MatrixCounter+1), "MatrixContainer::ParseMatrix: ***Matrix"); // one more each for the total molecule
   RowCounter = (int *) Malloc(sizeof(int)*(MatrixCounter+1), "MatrixContainer::ParseMatrix: *RowCounter");
+  for(int i=0;i<=MatrixCounter;i++) {
+    Matrix[i] = NULL;
+    RowCounter[i] = -1;
+  }
   for(int i=0;i<=MatrixCounter;i++) {
     // energy
@@ -498 +502 @@
   cout << "Parsing key sets." << endl;
   KeySets = (int **) Malloc(sizeof(int *)*FragmentCounter, "KeySetsContainer::ParseKeySets: **KeySets");
+  for(int i=0;i<FragmentCounter;i++)
+    KeySets[i] = NULL;
   line << name << FRAGMENTPREFIX << KEYSETFILE;
   input.open(line.str().c_str(), ios::in);
@@ -511 +517 @@
     // parse the values
     KeySets[i] = (int *) Malloc(sizeof(int)*AtomCounter[i], "KeySetsContainer::ParseKeySets: *KeySets[]");
+    for(int j=0;j<AtomCounter[i];j++)
+      KeySets[i][j] = -1;
     FragmentNumber = FixedDigitNumber(FragmentCounter, i);
     cout << FRAGMENTPREFIX << FragmentNumber << "[" << AtomCounter[i] << "]:";