Changeset a1d035 for src

Timestamp:

Apr 8, 2013, 11:56:18 AM (12 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:

356ae4

Parents:

569e42

git-author:

Frederik Heber <heber@…> (03/04/13 17:11:03)

git-committer:

Frederik Heber <heber@…> (04/08/13 11:56:18)

Message:

Converted TouchedList from int* to std::vector<int> in PowerSetGenerator.

• this is preparatory for removing use of local numbers from fragment KeySets.

Location:

src/Fragmentation

Files:

• PowerSetGenerator.cpp (modified) (9 diffs)
• PowerSetGenerator.hpp (modified) (1 diff)

src/Fragmentation/PowerSetGenerator.cpp

@@ -65 +65 @@
 /** Clears the touched list
  * \param verbosity verbosity level
- * \param *&TouchedList touched list
+ * \param &TouchedList touched list
  * \param SubOrder current suborder
  * \param TouchedIndex currently touched
  */
-void PowerSetGenerator::ClearingTouched(int verbosity, int *&TouchedList, int SubOrder, int &TouchedIndex)
+void PowerSetGenerator::ClearingTouched(int verbosity, TouchedList_t &TouchedList, int SubOrder, int &TouchedIndex)
 {
   LOG(1+verbosity, "Clearing touched list.");
+  TouchedList.resize(SubOrder+1, -1);
   for (TouchedIndex=SubOrder+1;TouchedIndex--;)  // empty touched list
     TouchedList[TouchedIndex] = -1;
   TouchedIndex = 0;
-
 }
 
@@ -84 +84 @@
  * \param *FragmentSet snake stack to remove from
  * \param &BondsSet set of bonds
- * \param *&TouchedList touched list
+ * \param &TouchedList touched list
  * \param TouchedIndex currently touched
  * \return number of set bits
  */
-int PowerSetGenerator::AddPowersetToSnakeStack(int verbosity, int CurrentCombination, int SetDimension, KeySet *FragmentSet, std::vector<bond::ptr > &BondsSet, int *&TouchedList, int &TouchedIndex)
+int PowerSetGenerator::AddPowersetToSnakeStack(int verbosity, int CurrentCombination, int SetDimension, KeySet *FragmentSet, std::vector<bond::ptr > &BondsSet, TouchedList_t &TouchedList, int &TouchedIndex)
 {
   atom *OtherWalker = NULL;
@@ -118 +118 @@
  * \param SetFirst begin iterator first bond
  * \param SetLast end iterator
- * \param *&TouchedList touched list
+ * \param &TouchedList touched list
  * \param TouchedIndex currently touched
  * \return number of elements
  */
-int PowerSetGenerator::CountSetMembers(std::list<bond::ptr >::const_iterator SetFirst, std::list<bond::ptr >::const_iterator SetLast, int *&TouchedList, int TouchedIndex)
+int PowerSetGenerator::CountSetMembers(std::list<bond::ptr >::const_iterator SetFirst, std::list<bond::ptr >::const_iterator SetLast, const TouchedList_t &TouchedList, int TouchedIndex)
 {
   int SetDimension = 0;
@@ -128 +128 @@
       Binder != SetLast;
       ++Binder) {
-    for (int k=TouchedIndex;k--;) {
-      if ((*Binder)->Contains(TouchedList[k]))   // if we added this very endpiece
+    for (TouchedList_t::const_iterator iter = TouchedList.begin();
+        iter != TouchedList.end(); ++iter) {
+      if ((*Binder)->Contains(*iter))   // if we added this very endpiece
         SetDimension++;
     }
@@ -140 +141 @@
  * \param SetFirst begin iterator first bond
  * \param SetLast end iterator
- * \param *&TouchedList touched list
+ * \param &TouchedList touched list
  * \param TouchedIndex currently touched
  * \return number of elements
  */
-int PowerSetGenerator::FillBondsList(std::vector<bond::ptr > &BondsList, std::list<bond::ptr >::const_iterator SetFirst, std::list<bond::ptr >::const_iterator SetLast, int *&TouchedList, int TouchedIndex)
+int PowerSetGenerator::FillBondsList(std::vector<bond::ptr > &BondsList, std::list<bond::ptr >::const_iterator SetFirst, std::list<bond::ptr >::const_iterator SetLast, const TouchedList_t &TouchedList, int TouchedIndex)
 {
   int SetDimension = 0;
@@ -150 +151 @@
       Binder != SetLast;
       ++Binder) {
-    for (int k=0;k<TouchedIndex;k++) {
-      if ((*Binder)->leftatom->getNr() == TouchedList[k])   // leftatom is always the closer one
+    for (TouchedList_t::const_iterator iter = TouchedList.begin();
+        iter != TouchedList.end(); ++iter) {
+      if ((*Binder)->leftatom->getNr() == *iter)   // leftatom is always the closer one
         BondsList[SetDimension++] = (*Binder);
     }
@@ -161 +163 @@
  * \param verbosity verbosity level
  * \param *FragmentSet snake stack to remove from
- * \param *&TouchedList touched list
- * \param TouchedIndex currently touched
- */
-void PowerSetGenerator::RemoveAllTouchedFromSnakeStack(int verbosity, KeySet *FragmentSet, int *&TouchedList, int &TouchedIndex)
-{
-  int Removal = 0;
-  for(int j=0;j<TouchedIndex;j++) {
-    Removal = TouchedList[j];
+ * \param &TouchedList touched list
+ * \param TouchedIndex currently touched
+ */
+void PowerSetGenerator::RemoveAllTouchedFromSnakeStack(int verbosity, KeySet *FragmentSet, TouchedList_t &TouchedList, int &TouchedIndex)
+{
+  for (TouchedList_t::iterator iter = TouchedList.begin();
+      iter != TouchedList.end();++iter) {
+    const int Removal = *iter;
     LOG(2+verbosity, "Removing item nr. " << Removal << " from snake stack.");
     FragmentSet->erase(Removal);
-    TouchedList[j] = -1;
+    (*iter) = -1;
   }
   std::stringstream output;
@@ -261 +263 @@
   int TouchedIndex, SubSetDimension, Added;
   int SpaceLeft;
-  int *TouchedList = new int[SubOrder + 1];
+  TouchedList_t TouchedList(SubOrder + 1, -1);
   KeySetTestPair TestKeySetInsert;
 
@@ -330 +332 @@
     }
   }
-  delete[](TouchedList);
   LOG(1+verbosity, "End of SPFragmentGenerator, " << RootDistance << " away from Root " << *FragmentSearch->getRoot() << " and SubOrder is " << SubOrder << ".");
 };

src/Fragmentation/PowerSetGenerator.hpp

@@ -29 +29 @@
   ~PowerSetGenerator();
 
+  typedef std::vector<int> TouchedList_t;
+
   void SPFragmentGenerator(int RootDistance, std::vector<bond::ptr > &BondsSet, int SetDimension, int SubOrder);
   int operator()(KeySet &RestrictedKeySet, const enum HydrogenTreatment treatment);
-  void RemoveAllTouchedFromSnakeStack(int verbosity, KeySet *FragmentSet, int *&TouchedList, int &TouchedIndex);
-  int FillBondsList(std::vector<bond::ptr > &BondsList, std::list<bond::ptr >::const_iterator SetFirst, std::list<bond::ptr >::const_iterator SetLast, int *&TouchedList, int TouchedIndex);
-  int CountSetMembers(std::list<bond::ptr >::const_iterator SetFirst, std::list<bond::ptr >::const_iterator SetLast, int *&TouchedList, int TouchedIndex);
-  int AddPowersetToSnakeStack(int verbosity, int CurrentCombination, int SetDimension, KeySet *FragmentSet, std::vector<bond::ptr > &BondsSet, int *&TouchedList, int &TouchedIndex);
-  void ClearingTouched(int verbosity, int *&TouchedList, int SubOrder, int &TouchedIndex);
+  void RemoveAllTouchedFromSnakeStack(int verbosity, KeySet *FragmentSet, TouchedList_t &TouchedList, int &TouchedIndex);
+  int FillBondsList(std::vector<bond::ptr > &BondsList, std::list<bond::ptr >::const_iterator SetFirst, std::list<bond::ptr >::const_iterator SetLast, const TouchedList_t &TouchedList, int TouchedIndex);
+  int CountSetMembers(std::list<bond::ptr >::const_iterator SetFirst, std::list<bond::ptr >::const_iterator SetLast, const TouchedList_t &TouchedList, int TouchedIndex);
+  int AddPowersetToSnakeStack(int verbosity, int CurrentCombination, int SetDimension, KeySet *FragmentSet, std::vector<bond::ptr > &BondsSet, TouchedList_t &TouchedList, int &TouchedIndex);
+  void ClearingTouched(int verbosity, TouchedList_t &TouchedList, int SubOrder, int &TouchedIndex);
 
 private: