Changeset ba1823

Timestamp:

Oct 25, 2011, 12:08:02 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:

d9a032

Parents:

708798

git-author:

Frederik Heber <heber@…> (10/18/11 09:12:25)

git-committer:

Frederik Heber <heber@…> (10/25/11 12:08:02)

Message:

Moved all helpers fragmentation functions into folder src/Fragmentation.

Location:

src

Files:

• Fragmentation/fragmentation_helpers.cpp (added)
• Fragmentation/fragmentation_helpers.hpp (added)
• Makefile.am (modified) (2 diffs)
• molecule_fragmentation.cpp (modified) (6 diffs)

src/Makefile.am

@@ -175 +175 @@
   moleculelist.cpp \
   molecule.cpp \
+  Fragmentation/fragmentation_helpers.cpp \
   molecule_fragmentation.cpp \
   molecule_geometry.cpp \
@@ -198 +199 @@
   graph.hpp \
   linkedcell.hpp \
+  Fragmentation/fragmentation_helpers.hpp \
   molecule.hpp \
   ThermoStatContainer.hpp \

src/molecule_fragmentation.cpp

@@ -29 +29 @@
 #include "config.hpp"
 #include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
+#include "Fragmentation/fragmentation_helpers.hpp"
 #include "Graph/BondGraph.hpp"
 #include "Graph/CheckAgainstAdjacencyFile.hpp"
@@ -36 +38 @@
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "molecule.hpp"
-#include "Element/periodentafel.hpp"
 #include "World.hpp"
 
@@ -64 +65 @@
   DoLog(1) && (Log() << Verbose(1) << "Upper limit for this subgraph is " << FragmentCount << " for " << NoNonHydrogen << " non-H atoms with maximum bond degree of " << c << "." << endl);
   return FragmentCount;
-};
-
-/** Scans a single line for number and puts them into \a KeySet.
- * \param *out output stream for debugging
- * \param *buffer buffer to scan
- * \param &CurrentSet filled KeySet on return
- * \return true - at least one valid atom id parsed, false - CurrentSet is empty
- */
-bool ScanBufferIntoKeySet(char *buffer, KeySet &CurrentSet)
-{
-  stringstream line;
-  int AtomNr;
-  int status = 0;
-
-  line.str(buffer);
-  while (!line.eof()) {
-    line >> AtomNr;
-    if (AtomNr >= 0) {
-      CurrentSet.insert(AtomNr);  // insert at end, hence in same order as in file!
-      status++;
-    } // else it's "-1" or else and thus must not be added
-  }
-  DoLog(1) && (Log() << Verbose(1) << "The scanned KeySet is ");
-  for(KeySet::iterator runner = CurrentSet.begin(); runner != CurrentSet.end(); runner++) {
-    DoLog(0) && (Log() << Verbose(0) << (*runner) << "\t");
-  }
-  DoLog(0) && (Log() << Verbose(0) << endl);
-  return (status != 0);
-};
-
-/** Parses the KeySet file and fills \a *FragmentList from the known molecule structure.
- * Does two-pass scanning:
- * -# Scans the keyset file and initialises a temporary graph
- * -# Scans TEFactors file and sets the TEFactor of each key set in the temporary graph accordingly
- * Finally, the temporary graph is inserted into the given \a FragmentList for return.
- * \param &path path to file
- * \param *FragmentList empty, filled on return
- * \return true - parsing successfully, false - failure on parsing (FragmentList will be NULL)
- */
-bool ParseKeySetFile(std::string &path, Graph *&FragmentList)
-{
-  bool status = true;
-  ifstream InputFile;
-  stringstream line;
-  GraphTestPair testGraphInsert;
-  int NumberOfFragments = 0;
-  string filename;
-
-  if (FragmentList == NULL) { // check list pointer
-    FragmentList = new Graph;
-  }
-
-  // 1st pass: open file and read
-  DoLog(1) && (Log() << Verbose(1) << "Parsing the KeySet file ... " << endl);
-  filename = path + KEYSETFILE;
-  InputFile.open(filename.c_str());
-  if (InputFile.good()) {
-    // each line represents a new fragment
-    char buffer[MAXSTRINGSIZE];
-    // 1. parse keysets and insert into temp. graph
-    while (!InputFile.eof()) {
-      InputFile.getline(buffer, MAXSTRINGSIZE);
-      KeySet CurrentSet;
-      if ((strlen(buffer) > 0) && (ScanBufferIntoKeySet(buffer, CurrentSet))) {  // if at least one valid atom was added, write config
-        testGraphInsert = FragmentList->insert(GraphPair (CurrentSet,pair<int,double>(NumberOfFragments++,1)));  // store fragment number and current factor
-        if (!testGraphInsert.second) {
-          DoeLog(0) && (eLog()<< Verbose(0) << "KeySet file must be corrupt as there are two equal key sets therein!" << endl);
-          performCriticalExit();
-        }
-      }
-    }
-    // 2. Free and done
-    InputFile.close();
-    InputFile.clear();
-    DoLog(1) && (Log() << Verbose(1) << "\t ... done." << endl);
-  } else {
-    DoLog(1) && (Log() << Verbose(1) << "\t ... File " << filename << " not found." << endl);
-    status = false;
-  }
-
-  return status;
-};
-
-/** Parses the TE factors file and fills \a *FragmentList from the known molecule structure.
- * -# Scans TEFactors file and sets the TEFactor of each key set in the temporary graph accordingly
- * \param *out output stream for debugging
- * \param *path path to file
- * \param *FragmentList graph whose nodes's TE factors are set on return
- * \return true - parsing successfully, false - failure on parsing
- */
-bool ParseTEFactorsFile(char *path, Graph *FragmentList)
-{
-  bool status = true;
-  ifstream InputFile;
-  stringstream line;
-  GraphTestPair testGraphInsert;
-  int NumberOfFragments = 0;
-  double TEFactor;
-  char filename[MAXSTRINGSIZE];
-
-  if (FragmentList == NULL) { // check list pointer
-    FragmentList = new Graph;
-  }
-
-  // 2nd pass: open TEFactors file and read
-  DoLog(1) && (Log() << Verbose(1) << "Parsing the TEFactors file ... " << endl);
-  sprintf(filename, "%s/%s%s", path, FRAGMENTPREFIX, TEFACTORSFILE);
-  InputFile.open(filename);
-  if (InputFile != NULL) {
-    // 3. add found TEFactors to each keyset
-    NumberOfFragments = 0;
-    for(Graph::iterator runner = FragmentList->begin();runner != FragmentList->end(); runner++) {
-      if (!InputFile.eof()) {
-        InputFile >> TEFactor;
-        (*runner).second.second = TEFactor;
-        DoLog(2) && (Log() << Verbose(2) << "Setting " << ++NumberOfFragments << " fragment's TEFactor to " << (*runner).second.second << "." << endl);
-      } else {
-        status = false;
-        break;
-      }
-    }
-    // 4. Free and done
-    InputFile.close();
-    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
-  } else {
-    DoLog(1) && (Log() << Verbose(1) << "File " << filename << " not found." << endl);
-    status = false;
-  }
-
-  return status;
-};
-
-/** Stores key sets to file.
- * \param KeySetList Graph with Keysets
- * \param &path path to file
- * \return true - file written successfully, false - writing failed
- */
-bool StoreKeySetFile(Graph &KeySetList, std::string &path)
-{
-  bool status =  true;
-  string line = path + KEYSETFILE;
-  ofstream output(line.c_str());
-
-  // open KeySet file
-  DoLog(1) && (Log() << Verbose(1) << "Saving key sets of the total graph ... ");
-  if(output.good()) {
-    for(Graph::iterator runner = KeySetList.begin(); runner != KeySetList.end(); runner++) {
-      for (KeySet::iterator sprinter = (*runner).first.begin();sprinter != (*runner).first.end(); sprinter++) {
-        if (sprinter != (*runner).first.begin())
-          output << "\t";
-        output << *sprinter;
-      }
-      output << endl;
-    }
-    DoLog(0) && (Log() << Verbose(0) << "done." << endl);
-  } else {
-    DoeLog(0) && (eLog()<< Verbose(0) << "Unable to open " << line << " for writing keysets!" << endl);
-    performCriticalExit();
-    status = false;
-  }
-  output.close();
-  output.clear();
-
-  return status;
-};
-
-
-/** Stores TEFactors to file.
- * \param *out output stream for debugging
- * \param KeySetList Graph with factors
- * \param *path path to file
- * \return true - file written successfully, false - writing failed
- */
-bool StoreTEFactorsFile(Graph &KeySetList, char *path)
-{
-  ofstream output;
-  bool status =  true;
-  string line;
-
-  // open TEFactors file
-  line = path;
-  line.append("/");
-  line += FRAGMENTPREFIX;
-  line += TEFACTORSFILE;
-  output.open(line.c_str(), ios::out);
-  DoLog(1) && (Log() << Verbose(1) << "Saving TEFactors of the total graph ... ");
-  if(output != NULL) {
-    for(Graph::iterator runner = KeySetList.begin(); runner != KeySetList.end(); runner++)
-      output << (*runner).second.second << endl;
-    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
-  } else {
-    DoLog(1) && (Log() << Verbose(1) << "failed to open " << line << "." << endl);
-    status = false;
-  }
-  output.close();
-
-  return status;
-};
-
-/** For a given graph, sorts KeySets into a (index, keyset) map.
- * \param *GlobalKeySetList list of keysets with global ids (valid in "this" molecule) needed for adaptive increase
- * \return map from index to keyset
- */
-map<int,KeySet> * GraphToIndexedKeySet(Graph *GlobalKeySetList)
-{
-  map<int,KeySet> *IndexKeySetList = new map<int,KeySet>;
-  for(Graph::iterator runner = GlobalKeySetList->begin(); runner != GlobalKeySetList->end(); runner++) {
-    IndexKeySetList->insert( pair<int,KeySet>(runner->second.first,runner->first) );
-  }
-  return IndexKeySetList;
-};
-
-/** Inserts a (\a No, \a value) pair into the list, overwriting present one.
- * Note if values are equal, No will decided on which is first
- * \param *out output stream for debugging
- * \param &AdaptiveCriteriaList list to insert into
- * \param &IndexedKeySetList list to find key set for a given index \a No
- * \param FragOrder current bond order of fragment
- * \param No index of keyset
- * \param value energy value
- */
-void InsertIntoAdaptiveCriteriaList(map<int, pair<double,int> > *AdaptiveCriteriaList, map<int,KeySet> &IndexKeySetList, int FragOrder, int No, double Value)
-{
-  map<int,KeySet>::iterator marker = IndexKeySetList.find(No);    // find keyset to Frag No.
-  if (marker != IndexKeySetList.end()) {  // if found
-    Value *= 1 + MYEPSILON*(*((*marker).second.begin()));     // in case of equal energies this makes them not equal without changing anything actually
-    // as the smallest number in each set has always been the root (we use global id to keep the doubles away), seek smallest and insert into AtomMask
-    pair <map<int, pair<double,int> >::iterator, bool> InsertedElement = AdaptiveCriteriaList->insert( make_pair(*((*marker).second.begin()), pair<double,int>( fabs(Value), FragOrder) ));
-    map<int, pair<double,int> >::iterator PresentItem = InsertedElement.first;
-    if (!InsertedElement.second) { // this root is already present
-      if ((*PresentItem).second.second < FragOrder)  // if order there is lower, update entry with higher-order term
-        //if ((*PresentItem).second.first < (*runner).first)    // as higher-order terms are not always better, we skip this part (which would always include this site into adaptive increase)
-        {  // if value is smaller, update value and order
-        (*PresentItem).second.first = fabs(Value);
-        (*PresentItem).second.second = FragOrder;
-        DoLog(2) && (Log() << Verbose(2) << "Updated element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl);
-      } else {
-        DoLog(2) && (Log() << Verbose(2) << "Did not update element " <<  (*PresentItem).first << " as " << FragOrder << " is less than or equal to " << (*PresentItem).second.second << "." << endl);
-      }
-    } else {
-      DoLog(2) && (Log() << Verbose(2) << "Inserted element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl);
-    }
-  } else {
-    DoLog(1) && (Log() << Verbose(1) << "No Fragment under No. " << No << "found." << endl);
-  }
-};
-
-/** Counts lines in file.
- * Note we are scanning lines from current position, not from beginning.
- * \param InputFile file to be scanned.
- */
-int CountLinesinFile(ifstream &InputFile)
-{
-  char *buffer = new char[MAXSTRINGSIZE];
-  int lines=0;
-
-  int PositionMarker = InputFile.tellg();  // not needed as Inputfile is copied, given by value, not by ref
-  // count the number of lines, i.e. the number of fragments
-  InputFile.getline(buffer, MAXSTRINGSIZE); // skip comment lines
-  InputFile.getline(buffer, MAXSTRINGSIZE);
-  while(!InputFile.eof()) {
-    InputFile.getline(buffer, MAXSTRINGSIZE);
-    lines++;
-  }
-  InputFile.seekg(PositionMarker, ios::beg);
-  delete[](buffer);
-  return lines;
-};
-
-
-/** Scans the adaptive order file and insert (index, value) into map.
- * \param &path path to ENERGYPERFRAGMENT file (may be NULL if Order is non-negative)
- * \param &IndexedKeySetList list to find key set for a given index \a No
- * \return adaptive criteria list from file
- */
-map<int, pair<double,int> > * ScanAdaptiveFileIntoMap(std::string &path, map<int,KeySet> &IndexKeySetList)
-{
-  map<int, pair<double,int> > *AdaptiveCriteriaList = new map<int, pair<double,int> >;
-  int No = 0, FragOrder = 0;
-  double Value = 0.;
-  char buffer[MAXSTRINGSIZE];
-  string filename = path + ENERGYPERFRAGMENT;
-  ifstream InputFile(filename.c_str());
-
-  if (InputFile.fail()) {
-    DoeLog(1) && (eLog() << Verbose(1) << "Cannot find file " << filename << "." << endl);
-    return AdaptiveCriteriaList;
-  }
-
-  if (CountLinesinFile(InputFile) > 0) {
-    // each line represents a fragment root (Atom::Nr) id and its energy contribution
-    InputFile.getline(buffer, MAXSTRINGSIZE); // skip comment lines
-    InputFile.getline(buffer, MAXSTRINGSIZE);
-    while(!InputFile.eof()) {
-      InputFile.getline(buffer, MAXSTRINGSIZE);
-      if (strlen(buffer) > 2) {
-        //Log() << Verbose(2) << "Scanning: " << buffer << endl;
-        stringstream line(buffer);
-        line >> FragOrder;
-        line >> ws >> No;
-        line >> ws >> Value; // skip time entry
-        line >> ws >> Value;
-        No -= 1;  // indices start at 1 in file, not 0
-        //Log() << Verbose(2) << " - yields (" << No << "," << Value << ", " << FragOrder << ")" << endl;
-
-        // clean the list of those entries that have been superceded by higher order terms already
-        InsertIntoAdaptiveCriteriaList(AdaptiveCriteriaList, IndexKeySetList, FragOrder, No, Value);
-      }
-    }
-    // close and done
-    InputFile.close();
-    InputFile.clear();
-  }
-
-  return AdaptiveCriteriaList;
-};
-
-/** Maps adaptive criteria list back onto (Value, (Root Nr., Order))
- * (i.e. sorted by value to pick the highest ones)
- * \param *out output stream for debugging
- * \param &AdaptiveCriteriaList list to insert into
- * \param *mol molecule with atoms
- * \return remapped list
- */
-map<double, pair<int,int> >  * ReMapAdaptiveCriteriaListToValue(map<int, pair<double,int> > *AdaptiveCriteriaList, molecule *mol)
-{
-  atom *Walker = NULL;
-  map<double, pair<int,int> > *FinalRootCandidates = new map<double, pair<int,int> > ;
-  DoLog(1) && (Log() << Verbose(1) << "Root candidate list is: " << endl);
-  for(map<int, pair<double,int> >::iterator runner = AdaptiveCriteriaList->begin(); runner != AdaptiveCriteriaList->end(); runner++) {
-    Walker = mol->FindAtom((*runner).first);
-    if (Walker != NULL) {
-      //if ((*runner).second.second >= Walker->AdaptiveOrder) { // only insert if this is an "active" root site for the current order
-      if (!Walker->MaxOrder) {
-        DoLog(2) && (Log() << Verbose(2) << "(" << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "])" << endl);
-        FinalRootCandidates->insert( make_pair( (*runner).second.first, pair<int,int>((*runner).first, (*runner).second.second) ) );
-      } else {
-        DoLog(2) && (Log() << Verbose(2) << "Excluding (" << *Walker << ", " << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "]), as it has reached its maximum order." << endl);
-      }
-    } else {
-      DoeLog(0) && (eLog()<< Verbose(0) << "Atom No. " << (*runner).second.first << " was not found in this molecule." << endl);
-      performCriticalExit();
-    }
-  }
-  return FinalRootCandidates;
-};
-
-/** Marks all candidate sites for update if below adaptive threshold.
- * Picks a given number of highest values and set *AtomMask to true.
- * \param *out output stream for debugging
- * \param *AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
- * \param FinalRootCandidates list candidates to check
- * \param Order desired order
- * \param *mol molecule with atoms
- * \return true - if update is necessary, false - not
- */
-bool MarkUpdateCandidates(bool *AtomMask, map<double, pair<int,int> > &FinalRootCandidates, int Order, molecule *mol)
-{
-  atom *Walker = NULL;
-  int No = -1;
-  bool status = false;
-  for(map<double, pair<int,int> >::iterator runner = FinalRootCandidates.upper_bound(pow(10.,Order)); runner != FinalRootCandidates.end(); runner++) {
-    No = (*runner).second.first;
-    Walker = mol->FindAtom(No);
-    //if (Walker->AdaptiveOrder < MinimumRingSize[Walker->getNr()]) {
-      DoLog(2) && (Log() << Verbose(2) << "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", setting entry " << No << " of Atom mask to true." << endl);
-      AtomMask[No] = true;
-      status = true;
-    //} else
-      //Log() << Verbose(2) << "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", however MinimumRingSize of " << MinimumRingSize[Walker->getNr()] << " does not allow further adaptive increase." << endl;
-  }
-  return status;
-};
-
-/** print atom mask for debugging.
- * \param *out output stream for debugging
- * \param *AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
- * \param AtomCount number of entries in \a *AtomMask
- */
-void PrintAtomMask(bool *AtomMask, int AtomCount)
-{
-  DoLog(2) && (Log() << Verbose(2) << "              ");
-  for(int i=0;i<AtomCount;i++)
-    DoLog(0) && (Log() << Verbose(0) << (i % 10));
-  DoLog(0) && (Log() << Verbose(0) << endl);
-  DoLog(2) && (Log() << Verbose(2) << "Atom mask is: ");
-  for(int i=0;i<AtomCount;i++)
-    DoLog(0) && (Log() << Verbose(0) << (AtomMask[i] ? "t" : "f"));
-  DoLog(0) && (Log() << Verbose(0) << endl);
 };
 
@@ -1045 +657 @@
 };
 
-
-/** 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
-};
-
 /** From a given set of Bond sorted by Shortest Path distance, create all possible fragments of size \a SetDimension.
  * -# loops over every possible combination (2^dimension of edge set)
@@ -1255 +746 @@
 };
 
-/** Allocates memory for UniqueFragments::BondsPerSPList.
- * \param *out output stream
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- * \param FragmentSearch UniqueFragments
- * \sa FreeSPList()
- */
-void InitialiseSPList(int Order, struct UniqueFragments &FragmentSearch)
-{
-  FragmentSearch.BondsPerSPList.resize(Order);
-  FragmentSearch.BondsPerSPCount = new int[Order];
-  for (int i=Order;i--;) {
-    FragmentSearch.BondsPerSPCount[i] = 0;
-  }
-};
-
-/** Free's memory for for UniqueFragments::BondsPerSPList.
- * \param *out output stream
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- * \param FragmentSearch UniqueFragments\
- * \sa InitialiseSPList()
- */
-void FreeSPList(int Order, struct UniqueFragments &FragmentSearch)
-{
-  delete[](FragmentSearch.BondsPerSPCount);
-};
-
-/** Sets FragmenSearch to initial value.
- * Sets UniqueFragments::ShortestPathList entries to zero, UniqueFragments::BondsPerSPCount to zero (except zero level to 1) and
- * adds initial bond UniqueFragments::Root to UniqueFragments::Root to UniqueFragments::BondsPerSPList
- * \param *out output stream
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- * \param FragmentSearch UniqueFragments
- * \sa FreeSPList()
- */
-void SetSPList(int Order, struct UniqueFragments &FragmentSearch)
-{
-  // prepare Label and SP arrays of the BFS search
-  FragmentSearch.ShortestPathList[FragmentSearch.Root->getNr()] = 0;
-
-  // prepare root level (SP = 0) and a loop bond denoting Root
-  for (int i=Order;i--;)
-    FragmentSearch.BondsPerSPCount[i] = 0;
-  FragmentSearch.BondsPerSPCount[0] = 1;
-  bond *Binder = new bond(FragmentSearch.Root, FragmentSearch.Root);
-  FragmentSearch.BondsPerSPList[0].push_back(Binder);
-};
-
-/** Resets UniqueFragments::ShortestPathList and cleans bonds from UniqueFragments::BondsPerSPList.
- * \param *out output stream
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- * \param FragmentSearch UniqueFragments
- * \sa InitialiseSPList()
- */
-void ResetSPList(int Order, struct UniqueFragments &FragmentSearch)
-{
-  DoLog(0) && (Log() << Verbose(0) << "Free'ing all found lists. and resetting index lists" << endl);
-  for(int i=Order;i--;) {
-    DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << ": ");
-    for (UniqueFragments::BondsPerSP::const_iterator iter = FragmentSearch.BondsPerSPList[i].begin();
-        iter != FragmentSearch.BondsPerSPList[i].end();
-        ++iter) {
-      // Log() << Verbose(0) << "Removing atom " << Binder->leftatom->getNr() << " and " << Binder->rightatom->getNr() << "." << endl; // make sure numbers are local
-      FragmentSearch.ShortestPathList[(*iter)->leftatom->getNr()] = -1;
-      FragmentSearch.ShortestPathList[(*iter)->rightatom->getNr()] = -1;
-    }
-    // delete added bonds
-    for (UniqueFragments::BondsPerSP::iterator iter = FragmentSearch.BondsPerSPList[i].begin();
-        iter != FragmentSearch.BondsPerSPList[i].end();
-        ++iter) {
-      delete(*iter);
-    }
-    FragmentSearch.BondsPerSPList[i].clear();
-    // also start and end node
-    DoLog(0) && (Log() << Verbose(0) << "cleaned." << endl);
-  }
-};
-
-
-/** Fills the Bonds per Shortest Path List and set the vertex labels.
- * \param *out output stream
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- * \param FragmentSearch UniqueFragments
- * \param *mol molecule with atoms and bonds
- * \param RestrictedKeySet Restricted vertex set to use in context of molecule
- */
-void FillSPListandLabelVertices(int Order, struct UniqueFragments &FragmentSearch, molecule *mol, KeySet RestrictedKeySet)
-{
-  // Actually, we should construct a spanning tree vom the root atom and select all edges therefrom and put them into
-  // according shortest path lists. However, we don't. Rather we fill these lists right away, as they do form a spanning
-  // tree already sorted into various SP levels. That's why we just do loops over the depth (CurrentSP) and breadth
-  // (EdgeinSPLevel) of this tree ...
-  // In another picture, the bonds always contain a direction by rightatom being the one more distant from root and hence
-  // naturally leftatom forming its predecessor, preventing the BFS"seeker" from continuing in the wrong direction.
-  int AtomKeyNr = -1;
-  atom *Walker = NULL;
-  atom *OtherWalker = NULL;
-  atom *Predecessor = NULL;
-  bond *Binder = NULL;
-  int RootKeyNr = FragmentSearch.Root->GetTrueFather()->getNr();
-  int RemainingWalkers = -1;
-  int SP = -1;
-
-  DoLog(0) && (Log() << Verbose(0) << "Starting BFS analysis ..." << endl);
-  for (SP = 0; SP < (Order-1); SP++) {
-    DoLog(1) && (Log() << Verbose(1) << "New SP level reached: " << SP << ", creating new SP list with " << FragmentSearch.BondsPerSPCount[SP] << " item(s)");
-    if (SP > 0) {
-      DoLog(0) && (Log() << Verbose(0) << ", old level closed with " << FragmentSearch.BondsPerSPCount[SP-1] << " item(s)." << endl);
-      FragmentSearch.BondsPerSPCount[SP] = 0;
-    } else
-      DoLog(0) && (Log() << Verbose(0) << "." << endl);
-
-    RemainingWalkers = FragmentSearch.BondsPerSPCount[SP];
-    for (UniqueFragments::BondsPerSP::const_iterator CurrentEdge = FragmentSearch.BondsPerSPList[SP].begin();
-        CurrentEdge != FragmentSearch.BondsPerSPList[SP].end();
-        ++CurrentEdge) { /// start till end of this SP level's list
-      RemainingWalkers--;
-      Walker = (*CurrentEdge)->rightatom;    // rightatom is always the one more distant
-      Predecessor = (*CurrentEdge)->leftatom;    // ... and leftatom is predecessor
-      AtomKeyNr = Walker->getNr();
-      DoLog(0) && (Log() << Verbose(0) << "Current Walker is: " << *Walker << " with nr " << Walker->getNr() << " and SP of " << SP << ", with " << RemainingWalkers << " remaining walkers on this level." << endl);
-      // check for new sp level
-      // go through all its bonds
-      DoLog(1) && (Log() << Verbose(1) << "Going through all bonds of Walker." << endl);
-      const BondList& ListOfBonds = Walker->getListOfBonds();
-      for (BondList::const_iterator Runner = ListOfBonds.begin();
-          Runner != ListOfBonds.end();
-          ++Runner) {
-        OtherWalker = (*Runner)->GetOtherAtom(Walker);
-        if ((RestrictedKeySet.find(OtherWalker->getNr()) != RestrictedKeySet.end())
-  #ifdef ADDHYDROGEN
-         && (OtherWalker->getType()->getAtomicNumber() != 1)
-  #endif
-                                                              ) {  // skip hydrogens and restrict to fragment
-          DoLog(2) && (Log() << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->getNr() << " in bond " << *(*Runner) << "." << endl);
-          // set the label if not set (and push on root stack as well)
-          if ((OtherWalker != Predecessor) && (OtherWalker->GetTrueFather()->getNr() > RootKeyNr)) { // only pass through those with label bigger than Root's
-            FragmentSearch.ShortestPathList[OtherWalker->getNr()] = SP+1;
-            DoLog(3) && (Log() << Verbose(3) << "Set Shortest Path to " << FragmentSearch.ShortestPathList[OtherWalker->getNr()] << "." << endl);
-            // add the bond in between to the SP list
-            Binder = new bond(Walker, OtherWalker); // create a new bond in such a manner, that bond::rightatom is always the one more distant
-            FragmentSearch.BondsPerSPList[SP+1].push_back(Binder);
-            FragmentSearch.BondsPerSPCount[SP+1]++;
-            DoLog(3) && (Log() << Verbose(3) << "Added its bond to SP list, having now " << FragmentSearch.BondsPerSPCount[SP+1] << " item(s)." << endl);
-          } else {
-            if (OtherWalker != Predecessor)
-              DoLog(3) && (Log() << Verbose(3) << "Not passing on, as index of " << *OtherWalker << " " << OtherWalker->GetTrueFather()->getNr() << " is smaller than that of Root " << RootKeyNr << "." << endl);
-            else
-              DoLog(3) && (Log() << Verbose(3) << "This is my predecessor " << *Predecessor << "." << endl);
-          }
-        } else Log() << Verbose(2) << "Is not in the restricted keyset or skipping hydrogen " << *OtherWalker << "." << endl;
-      }
-    }
-  }
-};
-
-/** prints the Bonds per Shortest Path list in UniqueFragments.
- * \param *out output stream
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- * \param FragmentSearch UniqueFragments
- */
-void OutputSPList(int Order, struct UniqueFragments &FragmentSearch)
-{
-  DoLog(0) && (Log() << Verbose(0) << "Printing all found lists." << endl);
-  for(int i=1;i<Order;i++) {    // skip the root edge in the printing
-    DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << "." << endl);
-    for (UniqueFragments::BondsPerSP::const_iterator Binder = FragmentSearch.BondsPerSPList[i].begin();
-        Binder != FragmentSearch.BondsPerSPList[i].end();
-        ++Binder) {
-      DoLog(2) && (Log() << Verbose(2) << *Binder << endl);
-    }
-  }
-};
-
-/** Simply counts all bonds in all UniqueFragments::BondsPerSPList lists.
- * \param *out output stream
- * \param Order bond order (limits BFS exploration and "number of digits" in power set generation
- * \param FragmentSearch UniqueFragments
- */
-int CountNumbersInBondsList(int Order, struct UniqueFragments &FragmentSearch)
-{
-  int SP = -1;  // the Root <-> Root edge must be subtracted!
-  for(int i=Order;i--;) { // sum up all found edges
-    for (UniqueFragments::BondsPerSP::const_iterator Binder = FragmentSearch.BondsPerSPList[i].begin();
-        Binder != FragmentSearch.BondsPerSPList[i].end();
-        ++Binder) {
-      SP++;
-    }
-  }
-  return SP;
-};
 
 /** Creates a list of all unique fragments of certain vertex size from a given graph \a Fragment for a given root vertex in the context of \a this molecule.
@@ -1510 +811 @@
 };
 
-bool KeyCompare::operator() (const KeySet SubgraphA, const KeySet SubgraphB) const
-{
-  //Log() << Verbose(0) << "my check is used." << endl;
-  if (SubgraphA.size() < SubgraphB.size()) {
-    return true;
-  } else {
-    if (SubgraphA.size() > SubgraphB.size()) {
-      return false;
-    } else {
-      KeySet::iterator IteratorA = SubgraphA.begin();
-      KeySet::iterator IteratorB = SubgraphB.begin();
-      while ((IteratorA != SubgraphA.end()) && (IteratorB != SubgraphB.end())) {
-        if ((*IteratorA) <  (*IteratorB))
-          return true;
-        else if ((*IteratorA) > (*IteratorB)) {
-            return false;
-          } // else, go on to next index
-        IteratorA++;
-        IteratorB++;
-      } // end of while loop
-    }// end of check in case of equal sizes
-  }
-  return false; // if we reach this point, they are equal
-};
-
-
-/** Combines all KeySets from all orders into single ones (with just unique entries).
- * \param *out output stream for debugging
- * \param *&FragmentList list to fill
- * \param ***FragmentLowerOrdersList
- * \param &RootStack stack with all root candidates (unequal to each atom in complete molecule if adaptive scheme is applied)
- * \param *mol molecule with atoms and bonds
- */
-int CombineAllOrderListIntoOne(Graph *&FragmentList, Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
-{
-  int RootNr = 0;
-  int RootKeyNr = 0;
-  int StartNr = 0;
-  int counter = 0;
-  int NumLevels = 0;
-  atom *Walker = NULL;
-
-  DoLog(0) && (Log() << Verbose(0) << "Combining the lists of all orders per order and finally into a single one." << endl);
-  if (FragmentList == NULL) {
-    FragmentList = new Graph;
-    counter = 0;
-  } else {
-    counter = FragmentList->size();
-  }
-
-  StartNr = RootStack.back();
-  do {
-    RootKeyNr = RootStack.front();
-    RootStack.pop_front();
-    Walker = mol->FindAtom(RootKeyNr);
-    NumLevels = 1 << (Walker->AdaptiveOrder - 1);
-    for(int i=0;i<NumLevels;i++) {
-      if (FragmentLowerOrdersList[RootNr][i] != NULL) {
-        InsertGraphIntoGraph(*FragmentList, (*FragmentLowerOrdersList[RootNr][i]), &counter);
-      }
-    }
-    RootStack.push_back(Walker->getNr());
-    RootNr++;
-  } while (RootKeyNr != StartNr);
-  return counter;
-};
-
-/** Free's memory allocated for all KeySets from all orders.
- * \param *out output stream for debugging
- * \param ***FragmentLowerOrdersList
- * \param &RootStack stack with all root candidates (unequal to each atom in complete molecule if adaptive scheme is applied)
- * \param *mol molecule with atoms and bonds
- */
-void FreeAllOrdersList(Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
-{
-  DoLog(1) && (Log() << Verbose(1) << "Free'ing the lists of all orders per order." << endl);
-  int RootNr = 0;
-  int RootKeyNr = 0;
-  int NumLevels = 0;
-  atom *Walker = NULL;
-  while (!RootStack.empty()) {
-    RootKeyNr = RootStack.front();
-    RootStack.pop_front();
-    Walker = mol->FindAtom(RootKeyNr);
-    NumLevels = 1 << (Walker->AdaptiveOrder - 1);
-    for(int i=0;i<NumLevels;i++) {
-      if (FragmentLowerOrdersList[RootNr][i] != NULL) {
-        delete(FragmentLowerOrdersList[RootNr][i]);
-      }
-    }
-    delete[](FragmentLowerOrdersList[RootNr]);
-    RootNr++;
-  }
-  delete[](FragmentLowerOrdersList);
-};
+