Changeset 6bd7e0 for src/Tesselation/boundary.cpp

Timestamp:

Jan 2, 2012, 1:34:28 PM (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:

d78531

Parents:

f55ae5

git-author:

Frederik Heber <heber@…> (12/19/11 16:46:11)

git-committer:

Frederik Heber <heber@…> (01/02/12 13:34:28)

Message:

Renamed old LinkedCell class to LinkedCell_deprecated.

• this is preparatory for a smooth transition to the new implementation.
• note that class LinkedCell and namespace LinkedCell bite each other so far.

File:

• src/Tesselation/boundary.cpp (modified) (12 diffs)

src/Tesselation/boundary.cpp

@@ -322 +322 @@
  * \param *BoundaryPts set of boundary points to use or NULL
  * \param *TesselStruct Tesselation filled with points, lines and triangles on boundary on return
- * \param *LCList atoms in LinkedCell list
+ * \param *LCList atoms in LinkedCell_deprecated list
  * \param *filename filename prefix for output of vertex data
  * \return *TesselStruct is filled with convex boundary and tesselation is stored under \a *filename.
  */
-void FindConvexBorder(const molecule* mol, Boundaries *BoundaryPts, Tesselation *&TesselStruct, const LinkedCell *LCList, const char *filename)
+void FindConvexBorder(const molecule* mol, Boundaries *BoundaryPts, Tesselation *&TesselStruct, const LinkedCell_deprecated *LCList, const char *filename)
 {
         Info FunctionInfo(__func__);
@@ -711 +711 @@
   GreatestDiameter = GetDiametersOfCluster(BoundaryPoints, mol, TesselStruct, IsAngstroem);
   PointCloudAdaptor< molecule > cloud(mol, mol->name);
-  LinkedCell *LCList = new LinkedCell(cloud, 10.);
-  FindConvexBorder(mol, BoundaryPoints, TesselStruct, (const LinkedCell *&)LCList, NULL);
+  LinkedCell_deprecated *LCList = new LinkedCell_deprecated(cloud, 10.);
+  FindConvexBorder(mol, BoundaryPoints, TesselStruct, (const LinkedCell_deprecated *&)LCList, NULL);
   delete (LCList);
   delete[] BoundaryPoints;
@@ -815 +815 @@
   double phi[NDIM];
   map<molecule *, Tesselation *> TesselStruct;
-  map<molecule *, LinkedCell *> LCList;
+  map<molecule *, LinkedCell_deprecated *> LCList;
 
   for (MoleculeList::iterator ListRunner = List->ListOfMolecules.begin(); ListRunner != List->ListOfMolecules.end(); ListRunner++)
@@ -821 +821 @@
       LOG(1, "Pre-creating linked cell lists for molecule " << *ListRunner << ".");
       PointCloudAdaptor< molecule > cloud(*ListRunner, (*ListRunner)->name);
-      LCList[(*ListRunner)] = new LinkedCell(cloud, 10.); // get linked cell list
+      LCList[(*ListRunner)] = new LinkedCell_deprecated(cloud, 10.); // get linked cell list
       LOG(1, "Pre-creating tesselation for molecule " << *ListRunner << ".");
       TesselStruct[(*ListRunner)] = NULL;
-      FindNonConvexBorder((*ListRunner), TesselStruct[(*ListRunner)], (const LinkedCell *&)LCList[(*ListRunner)], 5., NULL);
+      FindNonConvexBorder((*ListRunner), TesselStruct[(*ListRunner)], (const LinkedCell_deprecated *&)LCList[(*ListRunner)], 5., NULL);
     }
 
@@ -1017 +1017 @@
 /** Checks whether there are no atoms inside a sphere around \a CurrentPosition
  *  except those atoms present in \a *filler.
- *  If filler is NULL, then we just call LinkedCell::GetPointsInsideSphere() and
+ *  If filler is NULL, then we just call LinkedCell_deprecated::GetPointsInsideSphere() and
  *  check whether the return list is empty.
  * @param *filler
@@ -1024 +1024 @@
  */
 bool isSpaceAroundPointVoid(
-    LinkedCell *LC,
+    LinkedCell_deprecated *LC,
     molecule *filler,
     const double boundary,
@@ -1111 +1111 @@
   bool firstInsertion = true;
   const Box &Domain = World::getInstance().getDomain();
-  map<molecule *, LinkedCell *> LCList;
+  map<molecule *, LinkedCell_deprecated *> LCList;
   std::vector<molecule *> List = World::getInstance().getAllMolecules();
   MoleculeListClass *MolList = World::getInstance().getMolecules();
@@ -1119 +1119 @@
       LOG(1, "Pre-creating linked cell lists for molecule " << *ListRunner << ".");
       PointCloudAdaptor< molecule > cloud(*ListRunner, (*ListRunner)->name);
-      LCList[(*ListRunner)] = new LinkedCell(cloud, 10.); // get linked cell list
+      LCList[(*ListRunner)] = new LinkedCell_deprecated(cloud, 10.); // get linked cell list
     }
 
@@ -1169 +1169 @@
         // Check whether there is anything too close by and whether atom is outside of domain
         FillIt = true;
-        for (std::map<molecule *, LinkedCell *>::iterator ListRunner = LCList.begin(); ListRunner != LCList.end(); ++ListRunner) {
+        for (std::map<molecule *, LinkedCell_deprecated *>::iterator ListRunner = LCList.begin(); ListRunner != LCList.end(); ++ListRunner) {
           FillIt = FillIt && isSpaceAroundPointVoid(
               ListRunner->second,
@@ -1234 +1234 @@
   LOG(0, MolList->ListOfMolecules.size() << " molecules have been inserted.");
 
-  for (std::map<molecule *, LinkedCell *>::iterator ListRunner = LCList.begin(); !LCList.empty(); ListRunner = LCList.begin()) {
+  for (std::map<molecule *, LinkedCell_deprecated *>::iterator ListRunner = LCList.begin(); !LCList.empty(); ListRunner = LCList.begin()) {
     delete ListRunner->second;
     LCList.erase(ListRunner);
@@ -1244 +1244 @@
  * \param *mol molecule structure with Atom's and Bond's
  * \param *&TesselStruct Tesselation filled with points, lines and triangles on boundary on return
- * \param *&LCList atoms in LinkedCell list
+ * \param *&LCList atoms in LinkedCell_deprecated list
  * \param RADIUS radius of the virtual sphere
  * \param *filename filename prefix for output of vertex data
  * \return true - tesselation successful, false - tesselation failed
  */
-bool FindNonConvexBorder(molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LCList, const double RADIUS, const char *filename = NULL)
+bool FindNonConvexBorder(molecule* const mol, Tesselation *&TesselStruct, const LinkedCell_deprecated *&LCList, const double RADIUS, const char *filename = NULL)
 {
         Info FunctionInfo(__func__);
@@ -1272 +1272 @@
   PointCloudAdaptor< molecule > cloud(mol, mol->name);
   if (LCList == NULL) {
-    LCList = new LinkedCell(cloud, 2.*RADIUS);
+    LCList = new LinkedCell_deprecated(cloud, 2.*RADIUS);
     freeLC = true;
   }