Changeset 9758f7 for src/Fragmentation/KeySetsContainer.cpp

Timestamp:

Oct 18, 2011, 8:07:37 AM (14 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:

1b145f

Parents:

a9b86d

git-author:

Frederik Heber <heber@…> (09/16/11 16:24:18)

git-committer:

Frederik Heber <heber@…> (10/18/11 08:07:37)

Message:

Removed C arrays in KeySetsContainer and MatrixContainer.

• replaced by std::vector<>s.
• transition is so far very minimal, external (range) counters are still present.
• extracted allocation of memory into own block in MatrixContainer::parseMatrix().

File:

• src/Fragmentation/KeySetsContainer.cpp (modified) (8 diffs)

src/Fragmentation/KeySetsContainer.cpp

@@ -21 +21 @@
 
 #include <fstream>
+#include <sstream>
 
 #include "CodePatterns/Log.hpp"
@@ -32 +33 @@
  */
 KeySetsContainer::KeySetsContainer() :
-  KeySets(NULL),
-  AtomCounter(NULL),
   FragmentCounter(0),
   Order(0),
-  FragmentsPerOrder(0),
-  OrderSet(NULL)
+  FragmentsPerOrder(0)
 {};
 
@@ -43 +41 @@
  */
 KeySetsContainer::~KeySetsContainer() {
-  for(int i=FragmentCounter;i--;)
-    delete[](KeySets[i]);
-  for(int i=Order;i--;)
-    delete[](OrderSet[i]);
-  delete[](KeySets);
-  delete[](OrderSet);
-  delete[](AtomCounter);
-  delete[](FragmentsPerOrder);
+//  for(int i=FragmentCounter;i--;)
+//    delete[](KeySets[i]);
+//  for(int i=Order;i--;)
+//    delete[](OrderSet[i]);
+//  delete[](KeySets);
+//  delete[](OrderSet);
+//  delete[](AtomCounter);
+//  delete[](FragmentsPerOrder);
 };
 
@@ -59 +57 @@
  * \return parsing succesful
  */
-bool KeySetsContainer::ParseKeySets(const char *name, const int *ACounter, const int FCounter) {
+bool KeySetsContainer::ParseKeySets(const std::string name, const IntVector ACounter, const int FCounter) {
   ifstream input;
   char *FragmentNumber = NULL;
@@ -67 +65 @@
   FragmentCounter = FCounter;
   DoLog(0) && (Log() << Verbose(0) << "Parsing key sets." << endl);
-  KeySets = new int*[FragmentCounter];
-  for(int i=FragmentCounter;i--;)
-    KeySets[i] = NULL;
+  KeySets.resize(FragmentCounter);
   file << name << FRAGMENTPREFIX << KEYSETFILE;
   input.open(file.str().c_str(), ios::in);
@@ -77 +73 @@
   }
 
-  AtomCounter = new int[FragmentCounter];
+  AtomCounter.resize(FragmentCounter);
   for(int i=0;(i<FragmentCounter) && (!input.eof());i++) {
     stringstream line;
     AtomCounter[i] = ACounter[i];
     // parse the values
-    KeySets[i] = new int[AtomCounter[i]];
+    KeySets[i].resize(AtomCounter[i]);
     for(int j=AtomCounter[i];j--;)
       KeySets[i][j] = -1;
@@ -121 +117 @@
 
   // scan through all to determine fragments per order
-  FragmentsPerOrder = new int[Order];
-  for(int i=Order;i--;)
-    FragmentsPerOrder[i] = 0;
+  FragmentsPerOrder.resize(Order);
+//  for(int i=Order;i--;)
+//    FragmentsPerOrder[i] = 0;
   for(int i=FragmentCounter;i--;) {
     Counter=0;
@@ -135 +131 @@
 
   // scan through all to gather indices to each order set
-  OrderSet = new int*[Order];
+  OrderSet.resize(Order);
   for(int i=Order;i--;)
-    OrderSet[i] = new int[FragmentsPerOrder[i]];
+    OrderSet[i].resize(FragmentsPerOrder[i]);
   for(int i=Order;i--;)
     FragmentsPerOrder[i] = 0;