Changeset 339910 for src/MoleculeLeafClass.cpp

Timestamp:

Dec 3, 2012, 9:49:30 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:

de0af2

Parents:

b9401e

git-author:

Frederik Heber <heber@…> (09/19/12 14:32:32)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:49:30)

Message:

Fragmentation now operates on a single molecule.

• FragmentMolecule() does not continue on Subgraphs.
• shifted remaining functionality from MoleculeLeafClass to Fragmentation.
• FragmentList, KeySets, and RootStack are all just instances not arrays anymore.

File:

• src/MoleculeLeafClass.cpp (modified) (1 diff)

src/MoleculeLeafClass.cpp

@@ -116 +116 @@
 };
 
-/** Fills the root stack for sites to be used as root in fragmentation depending on order or adaptivity criteria
- * Again, as in \sa FillBondStructureFromReference steps recursively through each Leaf in this chain list of molecule's.
- * \param *out output stream for debugging
- * \param *&RootStack stack to be filled
- * \param AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site
- * \param &FragmentCounter counts through the fragments in this MoleculeLeafClass
- * \param saturation whether to treat hydrogen special or not
- * \return true - stack is non-empty, fragmentation necessary, false - stack is empty, no more sites to update
- */
-bool MoleculeLeafClass::FillRootStackForSubgraphs(KeyStack *&RootStack, const AtomMask_t &AtomMask, int &FragmentCounter, const enum HydrogenSaturation saturation)
-{
-  if (RootStack != NULL) {
-    // find first root candidates
-    if (&(RootStack[FragmentCounter]) != NULL) {
-      RootStack[FragmentCounter].clear();
-      for(molecule::const_iterator iter = Leaf->begin(); iter != Leaf->end(); ++iter) {
-        const atom * const Father = (*iter)->GetTrueFather();
-        if (AtomMask.isTrue(Father->getNr())) // apply mask
-          if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) // skip hydrogen
-            RootStack[FragmentCounter].push_front((*iter)->getNr());
-      }
-      if (next != NULL)
-        next->FillRootStackForSubgraphs(RootStack, AtomMask, ++FragmentCounter, saturation);
-    } else {
-      LOG(1, "Rootstack[" << FragmentCounter << "] is NULL.");
-      return false;
-    }
-    FragmentCounter--;
-    return true;
-  } else {
-    LOG(1, "Rootstack is NULL.");
-    return false;
-  }
-};
 
-/** The indices per keyset are compared to the respective father's Atom::Nr in each subgraph and thus put into \a **&FragmentList.
- * \param *out output stream fro debugging
- * \param *reference reference molecule with the bond structure to be copied
- * \param *KeySetList list with all keysets
- * \param *ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
- * \param **&FragmentList list to be allocated and returned
- * \param &FragmentCounter counts the fragments as we move along the list
- * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
- * \retuen true - success, false - failure
- */
-bool MoleculeLeafClass::AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, ListOfLocalAtoms_t *&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList)
-{
-  bool status = true;
-  int KeySetCounter = 0;
-
-  LOG(1, "Begin of AssignKeySetsToFragment.");
-  // fill ListOfLocalAtoms if NULL was given
-  if (!Leaf->FillListOfLocalAtoms(ListOfLocalAtoms[FragmentCounter], reference->getAtomCount())) {
-    LOG(1, "Filling of ListOfLocalAtoms failed.");
-    return false;
-  }
-
-  // allocate fragment list
-  if (FragmentList == NULL) {
-    KeySetCounter = Count();
-    FragmentList = new Graph*[KeySetCounter];
-    for (int i=0;i<KeySetCounter;i++)
-      FragmentList[i] = NULL;
-    KeySetCounter = 0;
-  }
-
-  if ((KeySetList != NULL) && (KeySetList->size() != 0)) { // if there are some scanned keysets at all
-    // assign scanned keysets
-    if (FragmentList[FragmentCounter] == NULL)
-      FragmentList[FragmentCounter] = new Graph;
-    KeySet *TempSet = new KeySet;
-    for (Graph::iterator runner = KeySetList->begin(); runner != KeySetList->end(); runner++) { // key sets contain global numbers!
-      if (ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*((*runner).first.begin()))->getNr()] != NULL) {// as we may assume that that bond structure is unchanged, we only test the first key in each set
-        // translate keyset to local numbers
-        for (KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
-          TempSet->insert(ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*sprinter)->getNr()]->getNr());
-        // insert into FragmentList
-        FragmentList[FragmentCounter]->insert(GraphPair(*TempSet, pair<int, double> (KeySetCounter++, (*runner).second.second)));
-      }
-      TempSet->clear();
-    }
-    delete (TempSet);
-    if (KeySetCounter == 0) {// if there are no keysets, delete the list
-      LOG(1, "KeySetCounter is zero, deleting FragmentList.");
-      delete (FragmentList[FragmentCounter]);
-    } else
-      LOG(1, KeySetCounter << " keysets were assigned to subgraph " << FragmentCounter << ".");
-    FragmentCounter++;
-    if (next != NULL)
-      next->AssignKeySetsToFragment(reference, KeySetList, ListOfLocalAtoms, FragmentList, FragmentCounter, FreeList);
-    FragmentCounter--;
-  } else
-    LOG(1, "KeySetList is NULL or empty.");
-
-  if ((FreeList) && (ListOfLocalAtoms != NULL)) {
-    // free the index lookup list
-    (ListOfLocalAtoms[FragmentCounter]).clear();
-  }
-  LOG(1, "End of AssignKeySetsToFragment.");
-  return status;
-};
-
-/** Translate list into global numbers (i.e. ones that are valid in "this" molecule, not in MolecularWalker->Leaf)
- * \param *out output stream for debugging
- * \param **FragmentList Graph with local numbers per fragment
- * \param &FragmentCounter counts the fragments as we move along the list
- * \param &TotalNumberOfKeySets global key set counter
- * \param &TotalGraph Graph to be filled with global numbers
- */
-void MoleculeLeafClass::TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph)
-{
-  LOG(1, "Begin of TranslateIndicesToGlobalIDs.");
-  KeySet *TempSet = new KeySet;
-  if (FragmentList[FragmentCounter] != NULL) {
-    for (Graph::iterator runner = FragmentList[FragmentCounter]->begin(); runner != FragmentList[FragmentCounter]->end(); runner++) {
-      for (KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
-        TempSet->insert((Leaf->FindAtom(*sprinter))->GetTrueFather()->getNr());
-      TotalGraph.insert(GraphPair(*TempSet, pair<int, double> (TotalNumberOfKeySets++, (*runner).second.second)));
-      TempSet->clear();
-    }
-    delete (TempSet);
-  } else {
-    LOG(1, "FragmentList is NULL.");
-  }
-  if (next != NULL)
-    next->TranslateIndicesToGlobalIDs(FragmentList, ++FragmentCounter, TotalNumberOfKeySets, TotalGraph);
-  FragmentCounter--;
-  LOG(1, "End of TranslateIndicesToGlobalIDs.");
-};
 
 /** Simply counts the number of items in the list, from given MoleculeLeafClass.