Changeset e73ad9a for src/molecule_fragmentation.cpp

Timestamp:

Mar 2, 2011, 9:53:08 PM (14 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:

1a4d4fe

Parents:

2e4105

git-author:

Frederik Heber <heber@…> (02/25/11 20:52:50)

git-committer:

Frederik Heber <heber@…> (03/02/11 21:53:08)

Message:

Moved CyclicStructureAnalysis from molecule_graph.cpp into own functor in Graph/.

• libMolecuilderGraph needed by libMolecuilderAction and libMolecuilder now.
• replacing call to CyclicStructureAnalysis in molecule::FragmentMolecule() required removing MinimumRingSize from ::FragmentBOSSANOVA() and ::CheckOrderAtSite().
• replaced call in DepthFirstSearchAction.

File:

• src/molecule_fragmentation.cpp (modified) (9 diffs)

src/molecule_fragmentation.cpp

@@ -29 +29 @@
 #include "config.hpp"
 #include "element.hpp"
+#include "Graph/BondGraph.hpp"
+#include "Graph/CyclicStructureAnalysis.hpp"
 #include "Helpers/helpers.hpp"
-#include "Graph/BondGraph.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "molecule.hpp"
@@ -456 +457 @@
  * \param *GlobalKeySetList list of keysets with global ids (valid in "this" molecule) needed for adaptive increase
  * \param Order desired Order if positive, desired exponent in threshold criteria if negative (0 is single-step)
- * \param *MinimumRingSize array of max. possible order to avoid loops
  * \param path path to ENERGYPERFRAGMENT file (may be NULL if Order is non-negative)
  * \return true - needs further fragmentation, false - does not need fragmentation
  */
-bool molecule::CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, std::string path)
+bool molecule::CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, std::string path)
 {
   bool status = false;
@@ -628 +628 @@
 {
   MoleculeListClass *BondFragments = NULL;
-  int *MinimumRingSize = new int[getAtomCount()];
   int FragmentCounter;
   MoleculeLeafClass *MolecularWalker = NULL;
@@ -675 +674 @@
 
   // analysis of the cycles (print rings, get minimum cycle length) for each subgraph
-  for(int i=getAtomCount();i--;)
-    MinimumRingSize[i] = getAtomCount();
   MolecularWalker = Subgraphs;
   const int LeafCount = Subgraphs->next->Count();
@@ -697 +694 @@
     MolecularWalker->Leaf->PickLocalBackEdges(ListOfAtoms, BackEdgeStack, LocalBackEdgeStack);
     DoLog(0) && (Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
-    MolecularWalker->Leaf->CyclicStructureAnalysis(LocalBackEdgeStack, MinimumRingSize);
+    CyclicStructureAnalysis CycleAnalysis;
+    CycleAnalysis(LocalBackEdgeStack);
+    CycleAnalysis.getMinimumRingSize();
     DoLog(0) && (Log() << Verbose(0) << "Done with Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
     delete(LocalBackEdgeStack);
@@ -725 +724 @@
   AtomMask[getAtomCount()] = false;
   FragmentationToDo = false;  // if CheckOrderAtSite just ones recommends fragmentation, we will save fragments afterwards
-  while ((CheckOrder = CheckOrderAtSite(AtomMask, ParsedFragmentList, Order, MinimumRingSize, prefix))) {
+  while ((CheckOrder = CheckOrderAtSite(AtomMask, ParsedFragmentList, Order, prefix))) {
     FragmentationToDo = FragmentationToDo || CheckOrder;
     AtomMask[getAtomCount()] = true;   // last plus one entry is used as marker that we have been through this loop once already in CheckOrderAtSite()
@@ -740 +739 @@
         // call BOSSANOVA method
         DoLog(0) && (Log() << Verbose(0) << endl << " ========== BOND ENERGY of subgraph " << FragmentCounter << " ========================= " << endl);
-        MolecularWalker->Leaf->FragmentBOSSANOVA(FragmentList[FragmentCounter], RootStack[FragmentCounter], MinimumRingSize);
+        MolecularWalker->Leaf->FragmentBOSSANOVA(FragmentList[FragmentCounter], RootStack[FragmentCounter]);
       } else {
         DoeLog(1) && (eLog()<< Verbose(1) << "Subgraph " << MolecularWalker << " has no atoms!" << endl);
@@ -751 +750 @@
   delete[](AtomMask);
   delete(ParsedFragmentList);
-  delete[](MinimumRingSize);
 
   // ==================================== End of FRAGMENTATION ============================================
@@ -1646 +1644 @@
  * \param Fragment&*List list of already present keystacks (adaptive scheme) or empty list
  * \param &RootStack stack with all root candidates (unequal to each atom in complete molecule if adaptive scheme is applied)
- * \param *MinimumRingSize minimum ring size for each atom (molecule::Atomcount)
  * \return pointer to Graph list
  */
-void molecule::FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize)
+void molecule::FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack)
 {
   Graph ***FragmentLowerOrdersList = NULL;