Changeset 9758f7 for src/Fragmentation/EnergyMatrix.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/EnergyMatrix.cpp (modified) (2 diffs)

src/Fragmentation/EnergyMatrix.cpp

@@ -35 +35 @@
 {
   DoLog(0) && (Log() << Verbose(0) << "Parsing energy indices." << endl);
-  Indices = new int*[MatrixCounter + 1];
+  Indices.resize(MatrixCounter + 1);
   for(int i=MatrixCounter+1;i--;) {
-    Indices[i] = new int[RowCounter[i]];
+    Indices[i].resize(RowCounter[i]);
     for(int j=RowCounter[i];j--;)
       Indices[i][j] = j;
@@ -93 +93 @@
     }
     // allocate last plus one matrix
-    DoLog(0) && (Log() << Verbose(0) << "Allocating last plus one matrix with " << (RowCounter[MatrixCounter]+1) << " rows and " << ColumnCounter[MatrixCounter] << " columns." << endl);
-    Matrix[MatrixCounter] = new double*[RowCounter[MatrixCounter] + 1];
+    if (Matrix[MatrixCounter].size() <= RowCounter[MatrixCounter] + 2)
+      Matrix[MatrixCounter].resize(RowCounter[MatrixCounter] + 1);
     for(int j=0;j<=RowCounter[MatrixCounter];j++)
-      Matrix[MatrixCounter][j] = new double[ColumnCounter[MatrixCounter]];
+      if (Matrix[MatrixCounter][j].size() <= ColumnCounter[MatrixCounter]+1)
+        Matrix[MatrixCounter][j].resize(ColumnCounter[MatrixCounter]);
 
     // try independently to parse global energysuffix file if present