Changeset 7daf73 for src

Timestamp:

Feb 9, 2016, 7:11:37 AM (9 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:

45b45d

Parents:

87cadb

git-author:

Frederik Heber <heber@…> (02/08/16 15:07:21)

git-committer:

Frederik Heber <heber@…> (02/09/16 07:11:37)

Message:

LinkedCell's LinkedList is now a vector and no longer a set.

• this was causing conflicts in tests as the order of the atoms/TesselPoints in the LinkedList returned by getAllNeighbors() would depend on the order in memory and not on the geometrical ordering or on the ids.
• TESTFIX: needed to replace use of insert() in (unit)tests by push_back. But all in all only Molecules Removal regression test's pdb file is affected.

Location:

src

Files:

• Analysis/analysis_correlation.cpp (modified) (4 diffs)
• LinkedCell/LinkedCell.cpp (modified) (2 diffs)
• LinkedCell/LinkedCell_View.cpp (modified) (2 diffs)
• LinkedCell/types.hpp (modified) (1 diff)
• LinkedCell/unittests/LinkedCellUnitTest.cpp (modified) (1 diff)
• LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) (2 diffs)

src/Analysis/analysis_correlation.cpp

@@ -323 +323 @@
   }
 
-  //!> typedef for an unsorted container, (output) compatible with STL algorithms
-  typedef std::vector<const TesselPoint *> LinkedVector;
-
   // create intersection (to know when to check for double-counting)
-  LinkedVector intersected_atoms(atoms_second.size(), NULL);
-  LinkedVector::iterator intersected_atoms_end =
+  LinkedCell::LinkedList intersected_atoms(atoms_second.size(), NULL);
+  LinkedCell::LinkedList::iterator intersected_atoms_end =
       std::set_intersection(
           atoms_first.begin(),atoms_first.end(),
           atoms_second.begin(), atoms_second.end(),
           intersected_atoms.begin());
-  const LinkedCell::LinkedList intersected_atoms_set(intersected_atoms.begin(), intersected_atoms_end);
+  intersected_atoms.erase(intersected_atoms_end, intersected_atoms.end());
+  std::sort(intersected_atoms.begin(), intersected_atoms.end());
 
   // get linked cell view
@@ -340 +338 @@
   // convert second to _sorted_ set
   LinkedCell::LinkedList atoms_second_set(atoms_second.begin(), atoms_second.end());
+  std::sort(atoms_second_set.begin(), atoms_second_set.end());
   LOG(2, "INFO: first set has " << atoms_first.size()
       << " and second set has " << atoms_second_set.size() << " atoms.");
@@ -353 +352 @@
         max_distance,
         Walker->getPosition());
+    std::sort(ListOfNeighbors.begin(), ListOfNeighbors.end());
     LOG(2, "INFO: There are " << ListOfNeighbors.size() << " neighbors.");
 
@@ -358 +358 @@
     // NOTE: STL algorithms do mostly not work on sorted container because reassignment
     // of a value may also require changing its position.
-    LinkedVector intersected_set(atoms_second.size(), NULL);
-    LinkedVector::iterator intersected_end =
+    LinkedCell::LinkedList intersected_set(atoms_second.size(), NULL);
+    LinkedCell::LinkedList::iterator intersected_end =
         std::set_intersection(
             ListOfNeighbors.begin(),ListOfNeighbors.end(),
             atoms_second_set.begin(), atoms_second_set.end(),
             intersected_set.begin());
+    intersected_set.erase(intersected_end, intersected_set.end());
+    std::sort(intersected_set.begin(), intersected_set.end());
     // count remaining elements
     LOG(2, "INFO: Intersection with second set has " << int(intersected_end - intersected_set.begin()) << " elements.");
     // we have some possible candidates, go through each
-    for (LinkedVector::const_iterator neighboriter = intersected_set.begin();
+    for (LinkedCell::LinkedList::const_iterator neighboriter = intersected_set.begin();
         neighboriter != intersected_end;
         ++neighboriter) {
       const TesselPoint * const OtherWalker = (*neighboriter);
-      LinkedCell::LinkedList::const_iterator equaliter = intersected_atoms_set.find(OtherWalker);
-      if ((equaliter !=  intersected_atoms_set.end()) && (OtherWalker <= Walker)) {
+      LinkedCell::LinkedList::const_iterator equaliter =
+          std::lower_bound(intersected_atoms.begin(), intersected_atoms.end(), OtherWalker);
+      if ((equaliter !=  intersected_atoms.end())
+          && (*equaliter == OtherWalker) // cause we only check lower_bound not equal due to sort
+          && (OtherWalker <= Walker)) {
         // present in both sets, assure that we are larger
         continue;

src/LinkedCell/LinkedCell.cpp

@@ -72 +72 @@
 void LinkedCell::LinkedCell::addPoint(const TesselPoint *point)
 {
-  insert(point);
+  push_back(point);
 }
 
@@ -84 +84 @@
 void LinkedCell::LinkedCell::deletePoint(const TesselPoint *point)
 {
-  LinkedList::iterator iter = find(point);
+  LinkedList::iterator iter = std::find(begin(), end(), point);
   ASSERT( iter != end(),
       "LinkedCell::LinkedCell::deletePoint() - "+toString(*point)+" not present in this cell.");

src/LinkedCell/LinkedCell_View.cpp

@@ -137 +137 @@
           LCmodel->applyBoundaryConditions(absolute_n);
         const LinkedCell &List = LCmodel->getCell(absolute_n);
-        LOG(3, "INFO: Current cell is " << neighbors.first << " plus " << n << ", yielding " << absolute_n << ".");
-        for (LinkedCell::const_iterator Runner = List.begin(); Runner != List.end(); Runner++)
-          TesselList.insert(*Runner);
+        LOG(4, "INFO: Current cell is " << neighbors.first << " plus " << n << ", yielding " << absolute_n << ".");
+        for (LinkedCell::const_iterator Runner = List.begin(); Runner != List.end(); Runner++) {
+          TesselList.push_back(*Runner);
+          LOG(5, "INFO: Inserting " << **Runner);
+        }
       }
   return TesselList;
@@ -154 +156 @@
   for (LinkedList::const_iterator iter = TesselList.begin(); iter != TesselList.end(); ++iter) {
     if (domain.periodicDistanceSquared(center, (*iter)->getPosition()) <= radius*radius)
-      ReturnList.insert(*iter);
+      ReturnList.push_back(*iter);
   }
 

src/LinkedCell/types.hpp

@@ -31 +31 @@
 
   //!> linked list of tesselpoints
-  typedef std::set<const TesselPoint *> LinkedList;
+  typedef std::vector<const TesselPoint *> LinkedList;
 
   //!> three-dimensional array of LinkedCell instances

src/LinkedCell/unittests/LinkedCellUnitTest.cpp

@@ -81 +81 @@
 
   // add a point
-  cell->insert(Walker);
+  cell->push_back(Walker);
   CPPUNIT_ASSERT_EQUAL((size_t)1, cell->size());
 

src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp

@@ -140 +140 @@
   for (PointSet::const_iterator iter = NodeList.begin(); iter != NodeList.end(); ++iter)
     if (center.DistanceSquared((*iter)->getPosition()) <= distance*distance) {
-      ComparisonList.insert(*iter);
+      ComparisonList.push_back(*iter);
       //std::cout << **iter << " is inside of " << center << " plus " << distance << "." << std::endl;
     }
@@ -177 +177 @@
   for (PointSet::const_iterator iter = NodeList.begin(); iter != NodeList.end(); ++iter)
     if (center.DistanceSquared((*iter)->getPosition()) <= distance*distance) {
-      ComparisonList.insert(*iter);
+      ComparisonList.push_back(*iter);
       //std::cout << **iter << " is inside of " << center << " plus " << distance << "." << std::endl;
     }