Changeset f67817f for src/Fragmentation

Timestamp:

Oct 25, 2011, 12:08:03 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:

d0b375b

Parents:

23fb72

git-author:

Frederik Heber <heber@…> (10/18/11 12:26:01)

git-committer:

Frederik Heber <heber@…> (10/25/11 12:08:03)

Message:

Extracted power set generation into own class PowerSetGenerator.

Location:

src/Fragmentation

Files:

• Makefile.am (modified) (2 diffs)
• PowerSetGenerator.cpp (added)
• PowerSetGenerator.hpp (added)
• fragmentation_helpers.cpp (modified) (1 diff)
• fragmentation_helpers.hpp (modified) (1 diff)

src/Fragmentation/Makefile.am

@@ -10 +10 @@
         Fragmentation/KeySetsContainer.cpp \
         Fragmentation/MatrixContainer.cpp \
+        Fragmentation/PowerSetGenerator.cpp \
         Fragmentation/UniqueFragments.cpp
 
@@ -15 +16 @@
         Fragmentation/defs.hpp \
         Fragmentation/EnergyMatrix.hpp \
+        Fragmentation/ForceMatrix.hpp \
         Fragmentation/fragmentation_helpers.hpp \
-        Fragmentation/ForceMatrix.hpp \
         Fragmentation/helpers.hpp \
         Fragmentation/HessianMatrix.hpp \
         Fragmentation/KeySetsContainer.hpp \
         Fragmentation/MatrixContainer.hpp \
+        Fragmentation/PowerSetGenerator.hpp \
         Fragmentation/UniqueFragments.hpp
 

src/Fragmentation/fragmentation_helpers.cpp

@@ -426 +426 @@
 
 
-/** Clears the touched list
- * \param *out output stream for debugging
- * \param verbosity verbosity level
- * \param *&TouchedList touched list
- * \param SubOrder current suborder
- * \param TouchedIndex currently touched
- */
-void SPFragmentGenerator_ClearingTouched(int verbosity, int *&TouchedList, int SubOrder, int &TouchedIndex)
-{
-  Log() << Verbose(1+verbosity) << "Clearing touched list." << endl;
-  for (TouchedIndex=SubOrder+1;TouchedIndex--;)  // empty touched list
-    TouchedList[TouchedIndex] = -1;
-  TouchedIndex = 0;
-
-}
-
-/** Adds the current combination of the power set to the snake stack.
- * \param *out output stream for debugging
- * \param verbosity verbosity level
- * \param CurrentCombination
- * \param SetDimension maximum number of bits in power set
- * \param *FragmentSet snake stack to remove from
- * \param &BondsSet set of bonds
- * \param *&TouchedList touched list
- * \param TouchedIndex currently touched
- * \return number of set bits
- */
-int AddPowersetToSnakeStack(int verbosity, int CurrentCombination, int SetDimension, KeySet *FragmentSet, std::vector<bond *> &BondsSet, int *&TouchedList, int &TouchedIndex)
-{
-  atom *OtherWalker = NULL;
-  bool bit = false;
-  KeySetTestPair TestKeySetInsert;
-
-  int Added = 0;
-  for (int j=0;j<SetDimension;j++) {  // pull out every bit by shifting
-    bit = ((CurrentCombination & (1 << j)) != 0);  // mask the bit for the j-th bond
-    if (bit) {  // if bit is set, we add this bond partner
-      OtherWalker = BondsSet[j]->rightatom;  // rightatom is always the one more distant, i.e. the one to add
-      //Log() << Verbose(1+verbosity) << "Current Bond is " << BondsSet[j] << ", checking on " << *OtherWalker << "." << endl;
-      Log() << Verbose(2+verbosity) << "Adding " << *OtherWalker << " with nr " << OtherWalker->getNr() << "." << endl;
-      TestKeySetInsert = FragmentSet->insert(OtherWalker->getNr());
-      if (TestKeySetInsert.second) {
-        TouchedList[TouchedIndex++] = OtherWalker->getNr();  // note as added
-        Added++;
-      } else {
-        Log() << Verbose(2+verbosity) << "This was item was already present in the keyset." << endl;
-      }
-    } else {
-      Log() << Verbose(2+verbosity) << "Not adding." << endl;
-    }
-  }
-  return Added;
-};
-
-/** Counts the number of elements in a power set.
- * \param SetFirst begin iterator first bond
- * \param SetLast end iterator
- * \param *&TouchedList touched list
- * \param TouchedIndex currently touched
- * \return number of elements
- */
-int CountSetMembers(std::list<bond *>::const_iterator SetFirst, std::list<bond *>::const_iterator SetLast, int *&TouchedList, int TouchedIndex)
-{
-  int SetDimension = 0;
-  for( std::list<bond *>::const_iterator Binder = SetFirst;
-      Binder != SetLast;
-      ++Binder) {
-    for (int k=TouchedIndex;k--;) {
-      if ((*Binder)->Contains(TouchedList[k]))   // if we added this very endpiece
-        SetDimension++;
-    }
-  }
-  return SetDimension;
-};
-
-/** Fills a list of bonds from another
- * \param *BondsList bonds array/vector to fill
- * \param SetFirst begin iterator first bond
- * \param SetLast end iterator
- * \param *&TouchedList touched list
- * \param TouchedIndex currently touched
- * \return number of elements
- */
-int FillBondsList(std::vector<bond *> &BondsList, std::list<bond *>::const_iterator SetFirst, std::list<bond *>::const_iterator SetLast, int *&TouchedList, int TouchedIndex)
-{
-  int SetDimension = 0;
-  for( std::list<bond *>::const_iterator Binder = SetFirst;
-      Binder != SetLast;
-      ++Binder) {
-    for (int k=0;k<TouchedIndex;k++) {
-      if ((*Binder)->leftatom->getNr() == TouchedList[k])   // leftatom is always the closer one
-        BondsList[SetDimension++] = (*Binder);
-    }
-  }
-  return SetDimension;
-};
-
-/** Remove all items that were added on this SP level.
- * \param *out output stream for debugging
- * \param verbosity verbosity level
- * \param *FragmentSet snake stack to remove from
- * \param *&TouchedList touched list
- * \param TouchedIndex currently touched
- */
-void RemoveAllTouchedFromSnakeStack(int verbosity, KeySet *FragmentSet, int *&TouchedList, int &TouchedIndex)
-{
-  int Removal = 0;
-  for(int j=0;j<TouchedIndex;j++) {
-    Removal = TouchedList[j];
-    Log() << Verbose(2+verbosity) << "Removing item nr. " << Removal << " from snake stack." << endl;
-    FragmentSet->erase(Removal);
-    TouchedList[j] = -1;
-  }
-  DoLog(2) && (Log() << Verbose(2) << "Remaining local nr.s on snake stack are: ");
-  for(KeySet::iterator runner = FragmentSet->begin(); runner != FragmentSet->end(); runner++)
-    DoLog(0) && (Log() << Verbose(0) << (*runner) << " ");
-  DoLog(0) && (Log() << Verbose(0) << endl);
-  TouchedIndex = 0; // set Index to 0 for list of atoms added on this level
-};
-
-
 bool KeyCompare::operator() (const KeySet SubgraphA, const KeySet SubgraphB) const
 {

src/Fragmentation/fragmentation_helpers.hpp

@@ -36 +36 @@
 bool MarkUpdateCandidates(bool *AtomMask, std::map<double, std::pair<int,int> > &FinalRootCandidates, int Order, molecule *mol);
 void PrintAtomMask(bool *AtomMask, int AtomCount);
-void SPFragmentGenerator_ClearingTouched(int verbosity, int *&TouchedList, int SubOrder, int &TouchedIndex);
-int AddPowersetToSnakeStack(int verbosity, int CurrentCombination, int SetDimension, KeySet *FragmentSet, std::vector<bond *> &BondsSet, int *&TouchedList, int &TouchedIndex);
-int CountSetMembers(std::list<bond *>::const_iterator SetFirst, std::list<bond *>::const_iterator SetLast, 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);
-void RemoveAllTouchedFromSnakeStack(int verbosity, KeySet *FragmentSet, int *&TouchedList, int &TouchedIndex);
 
 int CombineAllOrderListIntoOne(Graph *&FragmentList, Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol);