- Timestamp:
- Mar 22, 2013, 12:04:17 AM (12 years ago)
- 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)
- Location:
- src
- Files:
-
- 3 edited
Legend:
- Unmodified
- Added
- Removed
-
src/Box.cpp
rcf1183 r31021ab 214 214 215 215 void Box::internal_explode(const Vector &point,int n) const{ 216 internal_list.clear();216 // internal_list.clear(); 217 217 size_t list_index = 0; 218 218 … … 233 233 dims++; 234 234 } // 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); 236 238 237 239 if(!dims){ -
src/Graph/BondGraph.hpp
rcf1183 r31021ab 188 188 } 189 189 // get all elements 190 std::set< const element *> PresentElements = getElementSetFromNumbers(elements);190 const std::set< const element *> PresentElements = getElementSetFromNumbers(elements); 191 191 192 192 // count atoms in molecule = dimension of matrix (also give each unique name and continuous numbering) … … 194 194 if (counter > 1) { 195 195 LOG(1, "STATUS: Setting max bond distance."); 196 LOG(1, "STATUS: Creating LinkedCell structure for given " << counter << " atoms."); 196 197 LinkedCell::LinkedCell_View LC = getLinkedCell(getMaxPossibleBondDistance(PresentElements)); 197 198 198 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(); 202 203 203 204 unsigned int BondCount = 0; … … 243 244 << MinMaxDistanceSquared << "."); 244 245 } 245 246 246 } else { 247 247 LOG(5, "REJECT: Not Adding: Wrong order."); -
src/Graph/DepthFirstSearchAnalysis.cpp
rcf1183 r31021ab 402 402 std::stringstream output; 403 403 output << CurrentSubgraph; 404 LOG( 0, "STATUS: Disconnected subgraph ranges from " << OldGraphNr << " to "404 LOG(1, "INFO: Disconnected subgraph ranges from " << OldGraphNr << " to " 405 405 << CurrentGraphNr-1 << ": " << output.str()); 406 406
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