Changeset ca8bea for src/Fragmentation/Fragmentation.cpp

Timestamp:

Dec 3, 2012, 9:49:59 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:

dcbb5d

Parents:

de0af2

git-author:

Frederik Heber <heber@…> (09/20/12 12:37:12)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:49:59)

Message:

ExportGraph_ToFiles performs now the storing of the generated Graph to files.

• FragmentMolecule now fills an internal graph.
• ExportGraph_ToFiles gets graph in cstor and writes the contained KeySets to file on call of operator().

File:

• src/Fragmentation/Fragmentation.cpp (modified) (5 diffs)

src/Fragmentation/Fragmentation.cpp

@@ -57 +57 @@
 #include "Graph/ListOfLocalAtoms.hpp"
 #include "molecule.hpp"
-#include "MoleculeLeafClass.hpp"
-#include "MoleculeListClass.hpp"
-#include "Parser/FormatParserStorage.hpp"
 #include "World.hpp"
 
@@ -102 +99 @@
 int Fragmentation::FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, std::string prefix, DepthFirstSearchAnalysis &DFS)
 {
-  MoleculeListClass *BondFragments = NULL;
   std::fstream File;
   bool FragmentationToDo = true;
   bool CheckOrder = false;
-  Graph TotalGraph;     // graph with all keysets however local numbers
   int TotalNumberOfKeySets = 0;
   AtomMask_t AtomMask(atomids);
@@ -166 +161 @@
   TranslateIndicesToGlobalIDs(FragmentList, TotalNumberOfKeySets, TotalGraph);
 
-  // ===== 8b. gather keyset lists (graphs) from all subgraphs and transform into MoleculeListClass =====
-  //if (FragmentationToDo) {    // we should always store the fragments again as coordination might have changed slightly without changing bond structure
-  // allocate memory for the pointer array and transmorph graphs into full molecular fragments
-  BondFragments = new MoleculeListClass(World::getPointer());
-  int k=0;
-  for(Graph::iterator runner = TotalGraph.begin(); runner != TotalGraph.end(); runner++) {
-    KeySet test = (*runner).first;
-    LOG(0, "Fragment No." << (*runner).second.first << " with TEFactor " << (*runner).second.second << ".");
-    BondFragments->insert(StoreFragmentFromKeySet(test, World::getInstance().getConfig()));
-    k++;
-  }
-  LOG(0, k << "/" << BondFragments->ListOfMolecules.size() << " fragments generated from the keysets.");
-
-  // ===== 9. Save fragments' configuration and keyset files et al to disk ===
-  if (BondFragments->ListOfMolecules.size() != 0) {
-    // create the SortIndex from BFS labels to order in the config file
-    std::map<atomId_t, int> SortIndex;
-    CreateMappingLabelsToConfigSequence(SortIndex);
-
-    LOG(1, "Writing " << BondFragments->ListOfMolecules.size() << " possible bond fragmentation configs");
-    bool write_status = true;
-    for (std::vector<std::string>::const_iterator iter = typelist.begin();
-        iter != typelist.end();
-        ++iter) {
-      LOG(2, "INFO: Writing bond fragments for type " << (*iter) << ".");
-      write_status = write_status
-      && BondFragments->OutputConfigForListOfFragments(
-          prefix,
-          FormatParserStorage::getInstance().getTypeFromName(*iter));
-    }
-    if (write_status)
-      LOG(1, "All configs written.");
-    else
-      LOG(1, "Some config writing failed.");
-
-    // store force index reference file
-    BondFragments->StoreForcesFile(prefix, SortIndex);
-
-    // store keysets file
-    TotalGraph.StoreKeySetFile(prefix);
-
-    {
-      // store Adjacency file
-      std::string filename = prefix + ADJACENCYFILE;
-      mol->StoreAdjacencyToFile(filename);
-    }
-
-    // store Hydrogen saturation correction file
-    BondFragments->AddHydrogenCorrection(prefix);
-
-    // store adaptive orders into file
-    StoreOrderAtSiteFile(prefix);
-
-    // restore orbital and Stop values
-    //CalculateOrbitals(*configuration);
-  } else {
-    LOG(1, "FragmentList is zero on return, splitting failed.");
-  }
-  // remove all create molecules again from the World including their atoms
-  for (MoleculeList::iterator iter = BondFragments->ListOfMolecules.begin();
-      !BondFragments->ListOfMolecules.empty();
-      iter = BondFragments->ListOfMolecules.begin()) {
-    // remove copied atoms and molecule again
-    molecule *mol = *iter;
-    mol->removeAtomsinMolecule();
-    World::getInstance().destroyMolecule(mol);
-    BondFragments->ListOfMolecules.erase(iter);
-  }
-  delete(BondFragments);
+  LOG(1, "STATUS: We have created " << TotalGraph.size() << " fragments.");
+
+  // store adaptive orders into file
+  StoreOrderAtSiteFile(prefix);
+
   LOG(0, "End of bond fragmentation.");
-
   return ((int)(!FragmentationToDo)+1);    // 1 - continue, 2 - stop (no fragmentation occured)
 };
@@ -361 +291 @@
 };
 
-/** Stores a fragment from \a KeySet into \a molecule.
- * First creates the minimal set of atoms from the KeySet, then creates the bond structure from the complete
- * molecule and adds missing hydrogen where bonds were cut.
- * \param *out output stream for debugging messages
- * \param &Leaflet pointer to KeySet structure
- * \param IsAngstroem whether we have Ansgtroem or bohrradius
- * \return pointer to constructed molecule
- */
-molecule * Fragmentation::StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem)
-{
-  Info info(__func__);
-  ListOfLocalAtoms_t SonList;
-  molecule *Leaf = World::getInstance().createMolecule();
-
-  StoreFragmentFromKeySet_Init(mol, Leaf, Leaflet, SonList);
-  // create the bonds between all: Make it an induced subgraph and add hydrogen
-//  LOG(2, "Creating bonds from father graph (i.e. induced subgraph creation).");
-  CreateInducedSubgraphOfFragment(mol, Leaf, SonList, IsAngstroem);
-
-  //Leaflet->Leaf->ScanForPeriodicCorrection(out);
-  return Leaf;
-};
-
-
 /** Estimates by educated guessing (using upper limit) the expected number of fragments.
  * The upper limit is
@@ -556 +462 @@
 };
 
-/** Create a SortIndex to map from atomic labels to the sequence in which the atoms are given in the config file.
- * \param &SortIndex Mapping array of size molecule::AtomCount
- * \return true - success, false - failure of SortIndex alloc
- */
-bool Fragmentation::CreateMappingLabelsToConfigSequence(std::map<atomId_t, int> &SortIndex)
-{
-  if (!SortIndex.empty()) {
-    LOG(1, "SortIndex has " << SortIndex.size() << " entries and is not empty as expected.");
-    return false;
-  }
-
-  int AtomNo = 0;
-  for(molecule::const_iterator iter=mol->begin();iter!=mol->end();++iter){
-    const int id = (*iter)->getNr();
-#ifndef NDEBUG
-    std::pair<std::map<atomId_t, int>::const_iterator, bool> inserter =
-#endif
-    SortIndex.insert( std::make_pair(id, AtomNo++) );
-    ASSERT( inserter.second ,
-        "Fragmentation::CreateMappingLabelsToConfigSequence() - same SortIndex set twice.");
-  }
-
-  return true;
-};
-
-
-/** Initializes some value for putting fragment of \a *mol into \a *Leaf.
- * \param *mol total molecule
- * \param *Leaf fragment molecule
- * \param &Leaflet pointer to KeySet structure
- * \param SonList calloc'd list which atom of \a *Leaf is a son of which atom in \a *mol
- * \return number of atoms in fragment
- */
-int Fragmentation::StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList)
-{
-  atom *FatherOfRunner = NULL;
-
-  // first create the minimal set of atoms from the KeySet
-  int size = 0;
-  for(KeySet::iterator runner = Leaflet.begin(); runner != Leaflet.end(); runner++) {
-    FatherOfRunner = mol->FindAtom((*runner));  // find the id
-    SonList.insert( std::make_pair(FatherOfRunner->getNr(), Leaf->AddCopyAtom(FatherOfRunner) ) );
-    size++;
-  }
-  return size;
-};
-
-
-/** Creates an induced subgraph out of a fragmental key set, adding bonds and hydrogens (if treated specially).
- * \param *out output stream for debugging messages
- * \param *mol total molecule
- * \param *Leaf fragment molecule
- * \param IsAngstroem whether we have Ansgtroem or bohrradius
- * \param SonList list which atom of \a *Leaf is a son of which atom in \a *mol
- */
-void Fragmentation::CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem)
-{
-  bool LonelyFlag = false;
-  atom *OtherFather = NULL;
-  atom *FatherOfRunner = NULL;
-
-  // we increment the iter just before skipping the hydrogen
-  // as we use AddBond, we cannot have a const_iterator here
-  for (molecule::iterator iter = Leaf->begin(); iter != Leaf->end();) {
-    LonelyFlag = true;
-    FatherOfRunner = (*iter)->father;
-    ASSERT(FatherOfRunner,"Atom without father found");
-    if (SonList.find(FatherOfRunner->getNr()) != SonList.end())  {  // check if this, our father, is present in list
-      // create all bonds
-      const BondList& ListOfBonds = FatherOfRunner->getListOfBonds();
-      for (BondList::const_iterator BondRunner = ListOfBonds.begin();
-          BondRunner != ListOfBonds.end();
-          ++BondRunner) {
-        OtherFather = (*BondRunner)->GetOtherAtom(FatherOfRunner);
-        if (SonList.find(OtherFather->getNr()) != SonList.end()) {
-//          LOG(2, "INFO: Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->getNr()]
-//              << " is bound to " << *OtherFather << ", whose son is "
-//              << *SonList[OtherFather->getNr()] << ".");
-          if (OtherFather->getNr() > FatherOfRunner->getNr()) { // add bond (Nr check is for adding only one of both variants: ab, ba)
-            std::stringstream output;
-//            output << "ACCEPT: Adding Bond: "
-            output << Leaf->AddBond((*iter), SonList[OtherFather->getNr()], (*BondRunner)->BondDegree);
-//            LOG(3, output.str());
-            //NumBonds[(*iter)->getNr()]++;
-          } else {
-//            LOG(3, "REJECY: Not adding bond, labels in wrong order.");
-          }
-          LonelyFlag = false;
-        } else {
-//          LOG(2, "INFO: Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->getNr()]
-//              << " is bound to " << *OtherFather << ", who has no son in this fragment molecule.");
-          if (saturation == DoSaturate) {
-//          LOG(3, "ACCEPT: Adding Hydrogen to " << (*iter)->Name << " and a bond in between.");
-            if (!Leaf->AddHydrogenReplacementAtom((*BondRunner), (*iter), FatherOfRunner, OtherFather, IsAngstroem))
-              exit(1);
-          }
-          //NumBonds[(*iter)->getNr()] += Binder->BondDegree;
-        }
-      }
-    } else {
-    ELOG(1, "Son " << (*iter)->getName() << " has father " << FatherOfRunner->getName() << " but its entry in SonList is " << SonList[FatherOfRunner->getNr()] << "!");
-    }
-    if ((LonelyFlag) && (Leaf->getAtomCount() > 1)) {
-      LOG(0, **iter << "has got bonds only to hydrogens!");
-    }
-    ++iter;
-    if (saturation == DoSaturate) {
-      while ((iter != Leaf->end()) && ((*iter)->getType()->getAtomicNumber() == 1)){ // skip added hydrogen
-        iter++;
-      }
-    }
-  }
-};
-
-/** Sets the desired output types of the fragment configurations.
- *
- * @param types vector of desired types.
- */
-void Fragmentation::setOutputTypes(const std::vector<std::string> &types)
-{
-  typelist = types;
-}
-
 /** 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.