Changeset af2c424 for src/linkedcell.hpp

Timestamp:

Aug 28, 2010, 12:57:56 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:

c449d9

Parents:

21585f

git-author:

Frederik Heber <heber@…> (08/27/10 20:58:40)

git-committer:

Frederik Heber <heber@…> (08/28/10 00:57:56)

Message:

LinkedCell constructor rewritten.

• had to introduce getValue(iterator) to: molecule, tesselation, LinkedCell::LinkedNodes
• LinkedCell::LinkedNodes is not a typedef anymore
• new class LinkedCell::LinkedNodes derived from stl::list<TesselPoint *> to add getValue(iterator).
• LinkedCell constructors changed:
  • use template for all classes that have begin(), end() and ... sigh ... getValue()
  • Argh! STL containers do all have begin() and end() but no consistent operator* (maps return pair<> ...)
  • specialized version for PointCloud derivatives
  • various functions had to be changed due to changed signature of LinkedCell constructor

File:

• src/linkedcell.hpp (modified) (3 diffs)

src/linkedcell.hpp

@@ -22 +22 @@
 
 #include <list>
+#include <vector>
+#include <map>
 
+#include "Helpers/Assert.hpp"
+#include "Helpers/Log.hpp"
+#include "Helpers/Verbose.hpp"
 #include "defs.hpp"
+#include "World.hpp"
 #include "LinearAlgebra/Vector.hpp"
 
@@ -44 +50 @@
 
 public:
-  typedef list<TesselPoint *> LinkedNodes;
+  class LinkedNodes : public std::list<TesselPoint *> {
+  public:
+    LinkedNodes();
+    ~LinkedNodes();
+
+    TesselPoint * getValue (const_iterator &rhs) const;
+    TesselPoint * getValue (iterator &rhs) const;
+  };
+  //typedef list<TesselPoint *> LinkedNodes;
 
 
@@ -56 +70 @@
 
     LinkedCell();
-    LinkedCell(const  PointCloud * const set, const double RADIUS);
-    LinkedCell(LinkedNodes *set, const double radius);
+    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();
     const LinkedCell::LinkedNodes* GetCurrentCell()const ;