Changeset 88c8ec for src/Fragmentation

Timestamp:

Jan 17, 2013, 10:59:15 PM (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:

c8302f3

Parents:

d6b6ce

git-author:

Frederik Heber <heber@…> (10/29/12 00:28:46)

git-committer:

Frederik Heber <heber@…> (01/17/13 22:59:15)

Message:

REFACTOR: Replaced all "bond *" appearances by bond::ptr.

• this is preparatory for making bond::ptr a boost::shared_ptr of bond.
• NOTE: We had to remove a const prefix at four or five places and forward declarations had to be replaced by the true inclusion of bond.hpp at tne or so files. Apart from that, the replacement has been very smooth.

Location:

src/Fragmentation

Files:

• BondsPerShortestPath.cpp (modified) (2 diffs)
• PowerSetGenerator.cpp (modified) (5 diffs)
• PowerSetGenerator.hpp (modified) (2 diffs)

src/Fragmentation/BondsPerShortestPath.cpp

@@ -90 +90 @@
     BondsPerSPCount[i] = 0;
   BondsPerSPCount[0] = 1;
-  bond *Binder = new bond(_Root, _Root);
+  bond::ptr Binder = new bond(_Root, _Root);
   BondsPerSPList[0].push_back(Binder);
 };
@@ -138 +138 @@
   atom *OtherWalker = NULL;
   atom *Predecessor = NULL;
-  bond *Binder = NULL;
+  bond::ptr Binder = NULL;
   int RootKeyNr = _RootKeyNr;
   int RemainingWalkers = -1;

src/Fragmentation/PowerSetGenerator.cpp

@@ -88 +88 @@
  * \return number of set bits
  */
-int PowerSetGenerator::AddPowersetToSnakeStack(int verbosity, int CurrentCombination, int SetDimension, KeySet *FragmentSet, std::vector<bond *> &BondsSet, int *&TouchedList, int &TouchedIndex)
+int PowerSetGenerator::AddPowersetToSnakeStack(int verbosity, int CurrentCombination, int SetDimension, KeySet *FragmentSet, std::vector<bond::ptr > &BondsSet, int *&TouchedList, int &TouchedIndex)
 {
   atom *OtherWalker = NULL;
@@ -122 +122 @@
  * \return number of elements
  */
-int PowerSetGenerator::CountSetMembers(std::list<bond *>::const_iterator SetFirst, std::list<bond *>::const_iterator SetLast, int *&TouchedList, int TouchedIndex)
+int PowerSetGenerator::CountSetMembers(std::list<bond::ptr >::const_iterator SetFirst, std::list<bond::ptr >::const_iterator SetLast, int *&TouchedList, int TouchedIndex)
 {
   int SetDimension = 0;
-  for( std::list<bond *>::const_iterator Binder = SetFirst;
+  for( std::list<bond::ptr >::const_iterator Binder = SetFirst;
       Binder != SetLast;
       ++Binder) {
@@ -144 +144 @@
  * \return number of elements
  */
-int PowerSetGenerator::FillBondsList(std::vector<bond *> &BondsList, std::list<bond *>::const_iterator SetFirst, std::list<bond *>::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, int *&TouchedList, int TouchedIndex)
 {
   int SetDimension = 0;
-  for( std::list<bond *>::const_iterator Binder = SetFirst;
+  for( std::list<bond::ptr >::const_iterator Binder = SetFirst;
       Binder != SetLast;
       ++Binder) {
@@ -257 +257 @@
  * \param SubOrder remaining number of allowed vertices to add
  */
-void PowerSetGenerator::SPFragmentGenerator(int RootDistance, std::vector<bond *> &BondsSet, int SetDimension, int SubOrder)
+void PowerSetGenerator::SPFragmentGenerator(int RootDistance, std::vector<bond::ptr > &BondsSet, int SetDimension, int SubOrder)
 {
   Info info(__func__);
@@ -302 +302 @@
 
           // then allocate and fill the list
-          std::vector<bond *> BondsList;
+          std::vector<bond::ptr > BondsList;
           BondsList.resize(SubSetDimension);
           SubSetDimension = FillBondsList(BondsList, BondsPerSPList.BondsPerSPList[SP].begin(), BondsPerSPList.BondsPerSPList[SP].end(), TouchedList, TouchedIndex);

src/Fragmentation/PowerSetGenerator.hpp

@@ -17 +17 @@
 #include <vector>
 
+#include "Bond/bond.hpp"
 #include "Fragmentation/BondsPerShortestPath.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
 
-class bond;
 class UniqueFragments;
 
@@ -29 +29 @@
   ~PowerSetGenerator();
 
-  void SPFragmentGenerator(int RootDistance, std::vector<bond *> &BondsSet, int SetDimension, int SubOrder);
+  void SPFragmentGenerator(int RootDistance, std::vector<bond::ptr > &BondsSet, int SetDimension, int SubOrder);
   int operator()(KeySet &RestrictedKeySet, const enum HydrogenSaturation saturation);
   void RemoveAllTouchedFromSnakeStack(int verbosity, KeySet *FragmentSet, int *&TouchedList, int &TouchedIndex);
-  int FillBondsList(std::vector<bond *> &BondsList, std::list<bond *>::const_iterator SetFirst, std::list<bond *>::const_iterator SetLast, int *&TouchedList, int TouchedIndex);
-  int CountSetMembers(std::list<bond *>::const_iterator SetFirst, std::list<bond *>::const_iterator SetLast, int *&TouchedList, int TouchedIndex);
-  int AddPowersetToSnakeStack(int verbosity, int CurrentCombination, int SetDimension, KeySet *FragmentSet, std::vector<bond *> &BondsSet, 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);