Changeset de29ad6 for src/Graph

Timestamp:

Dec 28, 2011, 3:24:23 PM (13 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:

68c923

Parents:

bde4a6

git-author:

Frederik Heber <heber@…> (12/28/11 14:58:52)

git-committer:

Frederik Heber <heber@…> (12/28/11 15:24:23)

Message:

Some optimization to speed up Subgraph dissections.

• Replaced std::list by std::vector in VectorSet<>::minDistSquared() and Box::internal_explode() as it caused lots of dynamic allocation. This has been the main cause of the slowdown of Box::internal_explode().
• Box has internalized vector<int>s coords and index of internal_explode() to avoid dynamic allocation for them as well. This is worth it as it has a heavily used function.
• Made Box internal_list non-static. There is only one box anyway.
• changes caused in BoxUnitTest and Box cstor's and dstor.
• speedup of Subgraph

• enhanced verbosity of BondGraph::CreateAdjacency().

File:

• src/Graph/BondGraph.cpp (modified) (2 diffs)

src/Graph/BondGraph.cpp

@@ -197 +197 @@
                   const TesselPointSTLList *OtherList = LC.GetRelativeToCurrentCell(n);
                   if (OtherList != NULL) {
-                    LOG(3, "INFO: Current relative cell is " << LC.n[0] << ", " << LC.n[1] << ", " << LC.n[2] << " with No. " << LC.index << " containing " << List->size() << " points.");
+                    LOG(3, "INFO: Current relative cell is " << n[0] << ", " << n[1] << ", " << n[2] << " with No. " << LC.index << " containing " << List->size() << " points.");
                     for (TesselPointSTLList::const_iterator OtherRunner = OtherList->begin(); OtherRunner != OtherList->end(); OtherRunner++) {
                       if ((*OtherRunner) > Walker) {  // just to not add bonds from both sides
@@ -203 +203 @@
                         ASSERT(OtherWalker != NULL,
                             "BondGraph::CreateAdjacency() - TesselPoint that was not an atom retrieved from LinkedNode");
+                        LOG(3, "INFO: Current other atom is " << *OtherWalker << ".");
                         if (OtherWalker->father > Walker->father ) { // just to not add bonds from both sides
                           const range<double> MinMaxDistanceSquared(