Changeset 5d41b3f for src/LinkedCell

Timestamp:

Feb 22, 2012, 11:28:52 AM (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:

cbcda6

Parents:

ce81e76

git-author:

Frederik Heber <heber@…> (02/06/12 17:44:02)

git-committer:

Frederik Heber <heber@…> (02/22/12 11:28:52)

Message:

FIX: LinkedCell_Model::getStep() uses Box::WrapPeriodically() on given position.

• this is to "ensure" -- given correct BCs -- that index is inside domain.
• we still assert the index lateron (in case of Ignore BCs).

File:

• src/LinkedCell/LinkedCell_Model.cpp (modified) (4 diffs)

src/LinkedCell/LinkedCell_Model.cpp

@@ -289 +289 @@
 {
   tripleIndex index;
-  Vector x(Partition*position);
+  Vector x(Partition*domain.enforceBoundaryConditions(position));
   LOG(2, "INFO: Transformed position is " << x << ".");
   for (int i=0;i<NDIM;i++) {
@@ -450 +450 @@
 /** Calculates the interval bounds of the linked cell grid.
  *
- * \note we assume for index to allows be valid, i.e. within the range of LinkedCell_Model::N.
+ *  The neighborhood bounds works as follows: We give the lower, left, front
+ *  corner of the box and the number of boxes to go in each direction (i.e. the
+ *  relative upper, right, behind corner). We assure that the first corner is
+ *  within LinkedCell_Model::N, whether the relative second corner is within the
+ *  domain must be assured via applying its boundary conditions, see
+ *  LinkedCell_Model::applyBoundaryConditions()
+ *
+ * \note we check whether \a index is valid, i.e. within the range of LinkedCell_Model::N.
  *
  * \param index index to give relative bounds to
@@ -466 +473 @@
   for (size_t i=0;i<NDIM;++i) {
     ASSERT(index[i] >= 0,
-        "LinkedCell_Model::getNeighborhoodBounds() - index "+toString(index)+" out of lower bounds.");
+        "LinkedCell_Model::getNeighborhoodBounds() - index "
+        +toString(index)+" out of lower bounds.");
     ASSERT (index[i] < getSize(i),
-        "LinkedCell_Model::getNeighborhoodBounds() - index "+toString(index)+" out of upper bounds.");
+        "LinkedCell_Model::getNeighborhoodBounds() - index "
+        +toString(index)+" out of upper bounds.");
     switch (domain.getConditions()[i]) {
       case BoundaryConditions::Wrap:
@@ -505 +514 @@
         break;
     }
+    // check afterwards whether we now have correct
+    ASSERT((neighbors.first[i] >= 0) && (neighbors.first[i] < getSize(i)),
+        "LinkedCell_Model::getNeighborhoodBounds() - lower border "
+        +toString(neighbors.first)+" is out of bounds.");
   }
   LOG(3, "INFO: Resulting neighborhood bounds are [" << neighbors.first << "]<->[" << neighbors.second << "].");