Changeset 31021ab for src


Ignore:
Timestamp:
Mar 22, 2013, 12:04:17 AM (12 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:
d948b4
Parents:
cf1183
git-author:
Frederik Heber <heber@…> (03/01/13 19:25:36)
git-committer:
Frederik Heber <heber@…> (03/22/13 00:04:17)
Message:

Optimized Bondgraph detection.

  • VectorSet::minDistance() now operators on the set (translating by -point).
  • VectorSet::minDistSquared() removed as is the same as minDistance().
  • LinearAlgebra version is now 3:2:0, API is 1.0.5.
  • decrease log level of DepthFirstSearchAnalysis' msg about disconnected subgraphs.
  • Box::internal_explode() does not clear() internal_list, avoing constructing Vectors all the time.
  • BondGraph::CreateAdjacency gives some more message to tell when it does what.
Location:
src
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • src/Box.cpp

    rcf1183 r31021ab  
    214214
    215215void Box::internal_explode(const Vector &point,int n) const{
    216   internal_list.clear();
     216//  internal_list.clear();
    217217  size_t list_index = 0;
    218218
     
    233233    dims++;
    234234  } // there are max vectors in total we need to create
    235   internal_list.resize(pow(2*n+1, dims));
     235  const int new_size = pow(2*n+1, dims);
     236  if (internal_list.size() != new_size)
     237    internal_list.resize(new_size);
    236238
    237239  if(!dims){
  • src/Graph/BondGraph.hpp

    rcf1183 r31021ab  
    188188    }
    189189    // get all elements
    190     std::set< const element *> PresentElements = getElementSetFromNumbers(elements);
     190    const std::set< const element *> PresentElements = getElementSetFromNumbers(elements);
    191191
    192192    // count atoms in molecule = dimension of matrix (also give each unique name and continuous numbering)
     
    194194    if (counter > 1) {
    195195      LOG(1, "STATUS: Setting max bond distance.");
     196      LOG(1, "STATUS: Creating LinkedCell structure for given " << counter << " atoms.");
    196197      LinkedCell::LinkedCell_View LC = getLinkedCell(getMaxPossibleBondDistance(PresentElements));
    197198
    198       LOG(1, "STATUS: Creating LinkedCell structure for given " << counter << " atoms.");
    199 
    200       Box &domain = getDomain();
    201       unsigned int CurrentTime = getTime();
     199      LOG(1, "STATUS: Evaluating distance criterion for each atom.");
     200
     201      const Box &domain = getDomain();
     202      const unsigned int CurrentTime = getTime();
    202203
    203204      unsigned int BondCount = 0;
     
    243244                    << MinMaxDistanceSquared << ".");
    244245              }
    245 
    246246            } else {
    247247              LOG(5, "REJECT: Not Adding: Wrong order.");
  • src/Graph/DepthFirstSearchAnalysis.cpp

    rcf1183 r31021ab  
    402402    std::stringstream output;
    403403    output << CurrentSubgraph;
    404     LOG(0, "STATUS: Disconnected subgraph ranges from " << OldGraphNr << " to "
     404    LOG(1, "INFO: Disconnected subgraph ranges from " << OldGraphNr << " to "
    405405        << CurrentGraphNr-1 << ": " << output.str());
    406406
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