Changeset 061b06 for src

Timestamp:

Apr 20, 2010, 9:21:51 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:

f07f86d

Parents:

d5fea7

Message:

BUGFIXES: LinkedCell::SetIndexToNode() had wrong boundaries in zero case, LinkedCell::GetPointsInsideSphere() took only half the right radius

• BUGFIX: LinkedCell::SetIndexToNode() - upper and lower were set to 0 instead of n[i] when step=0 only worked
• BUGFIX: LinkedCell::GetPointsInsideSphere() called GetallNeighbours() with RADIUS instead if 2.*RADIUS

File:

• src/linkedcell.cpp (modified) (4 diffs)

src/linkedcell.cpp

@@ -280 +280 @@
  * \param *lower lower bounds
  * \param *upper upper bounds
+ * \param step how deep to check the neighbouring cells (i.e. number of layers to check)
  */
 void LinkedCell::GetNeighbourBounds(int lower[NDIM], int upper[NDIM], int step) const
 {
   for (int i=0;i<NDIM;i++) {
-    lower[i] = 0;
+    lower[i] = n[i];
     for (int s=step; s>0;--s)
       if ((n[i]-s) >= 0) {
@@ -290 +291 @@
         break;
       }
-    upper[i] = 0;
+    upper[i] = n[i];
     for (int s=step; s>0;--s)
       if ((n[i]+s) < N[i]) {
@@ -296 +297 @@
         break;
       }
-    //Log() << Verbose(0) << " [" << lower[i] << "," << upper[i] << "] ";
-    // check for this axis whether the point is outside of our grid
-    if (n[i] < 0)
-      upper[i] = lower[i];
-    if (n[i] > N[i])
-      lower[i] = upper[i];
-
     //Log() << Verbose(0) << "axis " << i << " has bounds [" << lower[i] << "," << upper[i] << "]" << endl;
   }
@@ -401 +395 @@
   // set index of LC to center of sphere
   const double dist = SetClosestIndexToOutsideVector(center);
-  if (dist > radius) {
+  if (dist > 2.*radius) {
     DoeLog(1) && (eLog()<< Verbose(1) << "Vector " << *center << " is too far away from any atom in LinkedCell's bounding box." << endl);
     return TesselList;
-  }
+  } else
+    Log() << Verbose(1) << "Distance of closest cell to center of sphere with radius " << radius << " is " << dist << "." << endl;
 
   // gather all neighbours first, then look who fulfills distance criteria
-  NeighbourList = GetallNeighbours(radius-dist);
+  NeighbourList = GetallNeighbours(2.*radius-dist);
+  //Log() << Verbose(1) << "I found " << NeighbourList->size() << " neighbours to check." << endl;
   if (NeighbourList != NULL) {
     for (LinkedNodes::const_iterator Runner = NeighbourList->begin(); Runner != NeighbourList->end(); Runner++) {
       Walker = *Runner;
+      //Log() << Verbose(1) << "Current neighbour is at " << *Walker->node << "." << endl;
       if ((center->DistanceSquared(Walker->node) - radiusSquared) < MYEPSILON) {
         TesselList->push_back(Walker);