Changeset 34c43a for src/linkedcell.cpp

Timestamp:

Mar 1, 2011, 10:16:38 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, Candidate_v1.7.0, 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:

caa06ef

Parents:

ba5215

git-author:

Frederik Heber <heber@…> (02/21/11 18:02:41)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:38)

Message:

Bigger change: Replaced PointCloud by PointCloudAdaptor.

• PointCloud is no more inherited by classes molecule and Tesselation but an interface to an (templated) adaptor called PointCloudAdaptor.
• As BoundaryPointSet only wraps TesselPoint member, we needed
• use CodePatterns/IteratorAdaptors.hpp to access the value (TesselPoint*) in the map Tesselation::BoundaryPointSet, requiring now v1.0.11.
• lots of places in Actions, Tesselation, and boundary had to be adapted to the new PointCloudAdaptor.
• LinkedCell also now only has constructor requesting a IPointCloud structure.
• this all will make BondGraph construction a lot easier (note that World has map containing atoms, where molecule has list. Hence, we need this IteratorAdaptor).
• TESTFIX: Marked Tesselation/Convex, Tesselation/NonConvex, and Tesselation/BigNonConvex as expected to fail due to wrong name in teecplot file. This is gonna be fixed in next issue.

File:

• src/linkedcell.cpp (modified) (10 diffs)

src/linkedcell.cpp

@@ -25 +25 @@
 #include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
-#include "PointCloud.hpp"
+#include "IPointCloud.hpp"
 #include "tesselation.hpp"
 #include "LinearAlgebra/Vector.hpp"
 
 // ========================================================= class LinkedCell ===========================================
-
-/** Constructor for class LinkedCell::LinkedNodes.
- */
-LinkedCell::LinkedNodes::LinkedNodes()
-{}
-
-/** Destructor for class LinkedCell::LinkedNodes.
- */
-LinkedCell::LinkedNodes::~LinkedNodes()
-{}
-
-TesselPoint * LinkedCell::LinkedNodes::getValue (const_iterator &rhs) const
-{
-  return *rhs;
-}
-
-TesselPoint * LinkedCell::LinkedNodes::getValue (iterator &rhs) const
-{
-  return *rhs;
-}
 
 /** Constructor for class LinkedCell.
@@ -68 +48 @@
  * \param RADIUS edge length of cells
  */
-LinkedCell::LinkedCell(const PointCloud & set, const double radius) :
+LinkedCell::LinkedCell(IPointCloud & set, const double radius) :
   LC(NULL),
   RADIUS(radius),
@@ -117 +97 @@
   }
   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]];
+  LC = new TesselPointSTLList[N[0]*N[1]*N[2]];
   for (index=0;index<N[0]*N[1]*N[2];index++) {
     LC [index].clear();
@@ -184 +164 @@
  * \return LinkedAtoms pointer to current cell, NULL if LinkedCell::n[] are out of bounds.
  */
-const LinkedCell::LinkedNodes* LinkedCell::GetCurrentCell() const
+const TesselPointSTLList* LinkedCell::GetCurrentCell() const
 {
   if (CheckBounds()) {
@@ -198 +178 @@
  * \return LinkedAtoms pointer to current cell, NULL if LinkedCell::n[]+relative[] are out of bounds.
  */
-const LinkedCell::LinkedNodes* LinkedCell::GetRelativeToCurrentCell(const int relative[NDIM]) const
+const TesselPointSTLList* LinkedCell::GetRelativeToCurrentCell(const int relative[NDIM]) const
 {
   if (CheckBounds(relative)) {
@@ -232 +212 @@
   index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
   if (CheckBounds()) {
-    for (LinkedNodes::iterator Runner = LC[index].begin(); Runner != LC[index].end(); Runner++)
+    for (TesselPointSTLList::iterator Runner = LC[index].begin(); Runner != LC[index].end(); Runner++)
       status = status || ((*Runner) == Walker);
     return status;
@@ -267 +247 @@
  * \return list of tesselpoints
  */
-LinkedCell::LinkedNodes* LinkedCell::GetallNeighbours(const double distance) const
+TesselPointSTLList* LinkedCell::GetallNeighbours(const double distance) const
 {
   int Nlower[NDIM], Nupper[NDIM];
   TesselPoint *Walker = NULL;
-  LinkedNodes *TesselList = new LinkedNodes;
+  TesselPointSTLList *TesselList = new TesselPointSTLList;
 
   // then go through the current and all neighbouring cells and check the contained points for possible candidates
@@ -281 +261 @@
     for (n[1] = Nlower[1]; n[1] <= Nupper[1]; n[1]++)
       for (n[2] = Nlower[2]; n[2] <= Nupper[2]; n[2]++) {
-        const LinkedNodes *List = GetCurrentCell();
+        const TesselPointSTLList *List = GetCurrentCell();
         //Log() << Verbose(1) << "Current cell is " << n[0] << ", " << n[1] << ", " << n[2] << " with No. " << index << "." << endl;
         if (List != NULL) {
-          for (LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
+          for (TesselPointSTLList::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
             Walker = *Runner;
             TesselList->push_back(Walker);
@@ -346 +326 @@
  * \return list of all points inside sphere
  */
-LinkedCell::LinkedNodes* LinkedCell::GetPointsInsideSphere(const double radius, const Vector * const center) const
+TesselPointSTLList* LinkedCell::GetPointsInsideSphere(const double radius, const Vector * const center) const
 {
   const double radiusSquared = radius*radius;
   TesselPoint *Walker = NULL;
-  LinkedNodes *TesselList = new LinkedNodes;
-  LinkedNodes *NeighbourList = NULL;
+  TesselPointSTLList *TesselList = new TesselPointSTLList;
+  TesselPointSTLList *NeighbourList = NULL;
 
   // set index of LC to center of sphere
@@ -365 +345 @@
   //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++) {
+    for (TesselPointSTLList::const_iterator Runner = NeighbourList->begin(); Runner != NeighbourList->end(); Runner++) {
       Walker = *Runner;
       //Log() << Verbose(1) << "Current neighbour is at " << *Walker->node << "." << endl;