Changeset 34c43a for src/linkedcell.hpp

Timestamp:

Mar 1, 2011, 10:16:38 AM (14 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:

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.hpp (modified) (5 diffs)

src/linkedcell.hpp

@@ -29 +29 @@
 #include "CodePatterns/Verbose.hpp"
 #include "Helpers/defs.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"
-#include "LinearAlgebra/Vector.hpp"
 
 /****************************************** forward declarations *****************************/
 
-class PointCloud;
+class IPointCloud;
 class TesselPoint;
 
@@ -44 +44 @@
 /********************************************** declarations *******************************/
 
+typedef std::list<TesselPoint *> TesselPointSTLList;
+
 /** Linked Cell class for containing Vectors in real space efficiently.
  */
@@ -50 +52 @@
 
 public:
-  class LinkedNodes : public std::list<TesselPoint *> {
-  public:
-    LinkedNodes();
-    ~LinkedNodes();
-
-    TesselPoint * getValue (const_iterator &rhs) const;
-    TesselPoint * getValue (iterator &rhs) const;
-  };
-  //typedef list<TesselPoint *> LinkedNodes;
-
-
     Vector max;       // upper boundary
     Vector min;       // lower boundary
-    LinkedNodes *LC;  // linked cell list
+    TesselPointSTLList *LC;  // linked cell list
     double RADIUS;    // cell edge length
     int N[NDIM];      // number of cells per axis
@@ -70 +61 @@
 
     LinkedCell();
-    LinkedCell(const PointCloud &set, const double radius);
-    template <class T> LinkedCell(const T &set, const double radius) :
-      LC(NULL),
-      RADIUS(radius),
-      index(-1)
-    {
-      class TesselPoint *Walker = NULL;
-      for(int i=0;i<NDIM;i++)
-        N[i] = 0;
-      max.Zero();
-      min.Zero();
-      DoLog(1) && (Log() << Verbose(1) << "Begin of LinkedCell" << endl);
-      if (set.begin() == set.end()) {
-        DoeLog(1) && (eLog()<< Verbose(1) << "set contains no linked cell nodes!" << endl);
-        return;
-      }
-      // 1. find max and min per axis of atoms
-      typename T::const_iterator Runner = set.begin();
-      for (int i=0;i<NDIM;i++) {
-        max[i] = set.getValue(Runner)->at(i);
-        min[i] = set.getValue(Runner)->at(i);
-      }
-      for (typename T::const_iterator Runner = set.begin(); Runner != set.end(); Runner++) {
-        Walker = set.getValue(Runner);
-        for (int i=0;i<NDIM;i++) {
-          if (max[i] < Walker->at(i))
-            max[i] = Walker->at(i);
-          if (min[i] > Walker->at(i))
-            min[i] = Walker->at(i);
-        }
-      }
-      DoLog(2) && (Log() << Verbose(2) << "Bounding box is " << min << " and " << max << "." << endl);
-
-      // 2. find then number of cells per axis
-      for (int i=0;i<NDIM;i++) {
-        N[i] = static_cast<int>(floor((max[i] - min[i])/RADIUS)+1);
-      }
-      DoLog(2) && (Log() << Verbose(2) << "Number of cells per axis are " << N[0] << ", " << N[1] << " and " << N[2] << "." << endl);
-
-      // 3. allocate the lists
-      DoLog(2) && (Log() << Verbose(2) << "Allocating cells ... ");
-      if (LC != NULL) {
-        DoeLog(1) && (eLog()<< Verbose(1) << "Linked Cell list is already allocated, I do nothing." << endl);
-        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++) {
-        LC [index].clear();
-      }
-      DoLog(0) && (Log() << Verbose(0) << "done."  << endl);
-
-      // 4. put each atom into its respective cell
-      DoLog(2) && (Log() << Verbose(2) << "Filling cells ... ");
-      for (typename T::const_iterator Runner = set.begin(); Runner != set.end(); Runner++) {
-        Walker = set.getValue(Runner);
-        for (int i=0;i<NDIM;i++) {
-          n[i] = static_cast<int>(floor((Walker->at(i) - min[i])/RADIUS));
-        }
-        index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
-        LC[index].push_back(Walker);
-        //Log() << Verbose(2) << *Walker << " goes into cell " << n[0] << ", " << n[1] << ", " << n[2] << " with No. " << index << "." << endl;
-      }
-      DoLog(0) && (Log() << Verbose(0) << "done."  << endl);
-      DoLog(1) && (Log() << Verbose(1) << "End of LinkedCell" << endl);
-    };
-
-
+    LinkedCell(IPointCloud &set, const double radius);
     ~LinkedCell();
-    const LinkedCell::LinkedNodes* GetCurrentCell()const ;
-    const LinkedCell::LinkedNodes* GetRelativeToCurrentCell(const int relative[NDIM])const ;
+    const TesselPointSTLList* GetCurrentCell()const ;
+    const TesselPointSTLList* GetRelativeToCurrentCell(const int relative[NDIM])const ;
     bool SetIndexToNode(const TesselPoint * const Walker)const ;
     bool SetIndexToVector(const Vector &x)const ;
@@ -148 +72 @@
     void GetNeighbourBounds(int lower[NDIM], int upper[NDIM], int step = 1)const ;
 
-    LinkedCell::LinkedNodes* GetallNeighbours(const double distance = 0) const;
-    LinkedCell::LinkedNodes* GetPointsInsideSphere(const double radius, const Vector * const center) const;
+    TesselPointSTLList* GetallNeighbours(const double distance = 0) const;
+    TesselPointSTLList* GetPointsInsideSphere(const double radius, const Vector * const center) const;
     // not implemented yet
     bool AddNode(Vector *Walker);