Changeset 0f4538 for src

Timestamp:

Aug 3, 2009, 4:45:38 PM (15 years ago)

Author:

Saskia Metzler <metzler@…>

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:

ee1b16

Parents:

9c20aa

Message:

new function LinkedCell::GetNeighbourBounds()

• LinkedCell::GetNeighbourBounds() needed as atom or vector to seek nearest neighbour for must not necessarily be contained in the LinkedCell grid itself. Hence, we have to use specific bounds for the NN search which this function returns.

Location:

src

Files:

• linkedcell.cpp (modified) (2 diffs)
• linkedcell.hpp (modified) (2 diffs)

src/linkedcell.cpp

@@ -129 +129 @@
 
 /** Calculates the index for a given atom *Walker.
- * \param *Walker atom to set index to
+ * \param Walker atom to set index to
  * \return if the atom is also found in this cell - true, else - false
  */
-bool LinkedCell::SetIndexToAtom(atom *Walker)
+bool LinkedCell::SetIndexToAtom(const atom &Walker)
 {
         bool status = false;
         for (int i=0;i<NDIM;i++) {
-                n[i] = (int)floor((Walker->x.x[i] - min.x[i])/RADIUS);
+                n[i] = (int)floor((Walker.x.x[i] - min.x[i])/RADIUS);
         }
+
         index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
         if (CheckBounds()) {
                 for (LinkedAtoms::iterator Runner = LC[index].begin(); Runner != LC[index].end(); Runner++)
-                        status = status || ((*Runner) == Walker);
+                        status = status || ((*Runner) == &Walker);
                 return status;
         } else {
-                cerr << Verbose(1) << "ERROR: Atom "<< *Walker << " at " << Walker->x << " is out of bounds." << endl;
+                cerr << Verbose(1) << "WARN: Atom "<< Walker << " at " << Walker.x << " is out of bounds." << endl;
                 return false;
         }
+};
+
+/** Calculates the interval bounds of the linked cell grid.
+ * \param *lower lower bounds
+ * \param *upper upper bounds
+ */
+void LinkedCell::GetNeighbourBounds(int lower[NDIM], int upper[NDIM])
+{
+  for (int i=0;i<NDIM;i++) {
+    lower[i] = ((n[i]-1) >= 0) ? n[i]-1 : 0;
+    upper[i] = ((n[i]+1) < N[i]) ? n[i]+1 : N[i]-1;
+    //cout << " [" << Nlower[i] << "," << Nupper[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];
+
+    //cout << "axis " << i << " has bounds [" << lower[i] << "," << upper[i] << "]" << endl;
+  }
 };
 
@@ -153 +174 @@
  * \return Vector is inside bounding box - true, else - false
  */
-bool LinkedCell::SetIndexToVector(Vector *x)
+bool LinkedCell::SetIndexToVector(const Vector *x)
 {
         bool status = true;

src/linkedcell.hpp

@@ -11 +11 @@
 #define LinkedAtoms list <atom *>
 
-class LinkedCell{
+class LinkedCell {
         public:
                 Vector max;                      // upper boundary
@@ -25 +25 @@
                 ~LinkedCell();
                 LinkedAtoms* GetCurrentCell();
-                bool SetIndexToAtom(atom *Walker);
-                bool SetIndexToVector(Vector *x);
+                bool SetIndexToAtom(const atom &Walker);
+                bool SetIndexToVector(const Vector *x);
+    void GetNeighbourBounds(int lower[NDIM], int upper[NDIM]);
                 bool CheckBounds();