Changeset c66537

Timestamp:

Aug 28, 2010, 12:57:56 AM (15 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:

73a857

Parents:

10fa1d

git-author:

Frederik Heber <heber@…> (08/27/10 09:30:34)

git-committer:

Frederik Heber <heber@…> (08/28/10 00:57:56)

Message:

FIX: changed minimal bondddistance threshold to 0.1, as otherwise molecular hydrogen is not scanned.

• introduced MAX_LINKEDCELLNODES in class LinkedCell as an upper bound for the number of cells allocated.

Location:

src

Files:

• linkedcell.cpp (modified) (2 diffs)
• linkedcell.hpp (modified) (1 diff)
• molecule_graph.cpp (modified) (1 diff)

src/linkedcell.cpp

@@ -96 +96 @@
     return;
   }
+  ASSERT(N[0]*N[1]*N[2] < MAX_LINKEDCELLNODES, "Number linked of linked cell nodes exceded hard-coded limit, use greater edge length!");
   LC = new LinkedNodes[N[0]*N[1]*N[2]];
   for (index=0;index<N[0]*N[1]*N[2];index++) {
@@ -168 +169 @@
     return;
   }
+  ASSERT(N[0]*N[1]*N[2] < MAX_LINKEDCELLNODES, "Number linked of linked cell nodes exceded hard-coded limit, use greater edge length!");
   LC = new LinkedNodes[N[0]*N[1]*N[2]];
   for (index=0;index<N[0]*N[1]*N[2];index++) {

src/linkedcell.hpp

@@ -33 +33 @@
 /********************************************** definitions *********************************/
 
+//< Upper bound for number of cell nodes used in sensibility check on allocation.
+enum { MAX_LINKEDCELLNODES = 1000000 };
 
 /********************************************** declarations *******************************/

src/molecule_graph.cpp

@@ -154 +154 @@
   DoLog(1) && (Log() << Verbose(1) << "AtomCount " << getAtomCount() << " and bonddistance is " << bonddistance << "." << endl);
 
-  if ((getAtomCount() > 1) && (bonddistance > 1.)) {
+  if ((getAtomCount() > 1) && (bonddistance > 0.1)) {
     DoLog(2) && (Log() << Verbose(2) << "Creating Linked Cell structure ... " << endl);
     LC = new LinkedCell(this, bonddistance);