Changeset a03d25

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:

f6d1d0

Parents:

d9a032

git-author:

Frederik Heber <heber@…> (10/18/11 11:53:21)

git-committer:

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

Message:

Placed all routines working on UniqueFragments struct inside this class.

• changed struct to class.

Location:

src

Files:

• Fragmentation/Makefile.am (modified) (2 diffs)
• Fragmentation/UniqueFragments.cpp (added)
• Fragmentation/UniqueFragments.hpp (added)
• Fragmentation/fragmentation_helpers.cpp (modified) (1 diff)
• Fragmentation/fragmentation_helpers.hpp (modified) (1 diff)
• graph.cpp (modified) (1 diff)
• graph.hpp (modified) (2 diffs)
• molecule_fragmentation.cpp (modified) (8 diffs)

src/Fragmentation/Makefile.am

@@ -9 +9 @@
         Fragmentation/HessianMatrix.cpp \
         Fragmentation/KeySetsContainer.cpp \
-        Fragmentation/MatrixContainer.cpp
+        Fragmentation/MatrixContainer.cpp \
+        Fragmentation/UniqueFragments.cpp
 
 FRAGMENTATIONHEADER = \
@@ -19 +20 @@
         Fragmentation/HessianMatrix.hpp \
         Fragmentation/KeySetsContainer.hpp \
-        Fragmentation/MatrixContainer.hpp
+        Fragmentation/MatrixContainer.hpp \
+        Fragmentation/UniqueFragments.hpp
 
 

src/Fragmentation/fragmentation_helpers.cpp

@@ -546 +546 @@
 };
 
-/** 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;
-};
 
 bool KeyCompare::operator() (const KeySet SubgraphA, const KeySet SubgraphB) const

src/Fragmentation/fragmentation_helpers.hpp

@@ -41 +41 @@
 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);
-void InitialiseSPList(int Order, struct UniqueFragments &FragmentSearch);
-void FreeSPList(int Order, struct UniqueFragments &FragmentSearch);
-void SetSPList(int Order, struct UniqueFragments &FragmentSearch);
-void ResetSPList(int Order, struct UniqueFragments &FragmentSearch);
-void FillSPListandLabelVertices(int Order, struct UniqueFragments &FragmentSearch, molecule *mol, KeySet RestrictedKeySet);
-void OutputSPList(int Order, struct UniqueFragments &FragmentSearch);
-int CountNumbersInBondsList(int Order, struct UniqueFragments &FragmentSearch);
+
 int CombineAllOrderListIntoOne(Graph *&FragmentList, Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol);
 void FreeAllOrdersList(Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol);

src/graph.cpp

@@ -87 +87 @@
 //};
 
-/** Checking whether KeySet is not already present in Graph, if so just adds factor.
- * \param *out output stream for debugging
- * \param &set KeySet to insert
- * \param &graph Graph to insert into
- * \param *counter pointer to unique fragment count
- * \param factor energy factor for the fragment
- */
-void InsertFragmentIntoGraph(struct UniqueFragments *Fragment)
-{
-  GraphTestPair testGraphInsert;
-
-  testGraphInsert = Fragment->Leaflet->insert(GraphPair (*Fragment->FragmentSet,pair<int,double>(Fragment->FragmentCounter,Fragment->TEFactor)));  // store fragment number and current factor
-  if (testGraphInsert.second) {
-    DoLog(2) && (Log() << Verbose(2) << "KeySet " << Fragment->FragmentCounter << " successfully inserted." << endl);
-    Fragment->FragmentCounter++;
-  } else {
-    DoLog(2) && (Log() << Verbose(2) << "KeySet " << Fragment->FragmentCounter << " failed to insert, present fragment is " << ((*(testGraphInsert.first)).second).first << endl);
-    ((*(testGraphInsert.first)).second).second += Fragment->TEFactor;  // increase the "created" counter
-    DoLog(2) && (Log() << Verbose(2) << "New factor is " << ((*(testGraphInsert.first)).second).second << "." << endl);
-  }
-};
 //void inline InsertIntoGraph(KeyStack &stack, Graph &graph, int *counter, double factor)
 //{

src/graph.hpp

@@ -31 +31 @@
 class Node;
 class Edge;
+class UniqueFragments;
 
 /********************************************** definitions *********************************/
@@ -56 +57 @@
 
 //bool operator < (KeySet SubgraphA, KeySet SubgraphB);   //note: this declaration is important, otherwise normal < is used (producing wrong order)
-void InsertFragmentIntoGraph(struct UniqueFragments *Fragment); // Insert a KeySet into a Graph
 void InsertGraphIntoGraph(Graph &graph1, Graph &graph2, int *counter);  // Insert all KeySet's in a Graph into another Graph
 
-/** Structure containing all values in power set combination generation.
- */
-struct UniqueFragments {
-  typedef std::list<bond*> BondsPerSP;
-  typedef std::vector< BondsPerSP > AllSPBonds;
-
-  config *configuration;
-  atom *Root;
-  Graph *Leaflet;
-  KeySet *FragmentSet;
-  int ANOVAOrder;
-  int FragmentCounter;
-  int CurrentIndex;
-  double TEFactor;
-  int *ShortestPathList;
-  bool **UsedList;
-  AllSPBonds BondsPerSPList;
-  int *BondsPerSPCount;
-};
 
 /********************************************** declarations *******************************/

src/molecule_fragmentation.cpp

@@ -31 +31 @@
 #include "Element/periodentafel.hpp"
 #include "Fragmentation/fragmentation_helpers.hpp"
+#include "Fragmentation/UniqueFragments.hpp"
 #include "Graph/BondGraph.hpp"
 #include "Graph/CheckAgainstAdjacencyFile.hpp"
@@ -732 +733 @@
           DoLog(0) && (Log() << Verbose(0) << (*runner) << " ");
         DoLog(0) && (Log() << Verbose(0) << endl);
-        InsertFragmentIntoGraph(FragmentSearch);
+        FragmentSearch->InsertFragmentIntoGraph();
       }
 
@@ -769 +770 @@
   DoLog(0) && (Log() << Verbose(0) << "Begin of PowerSetGenerator with order " << Order << " at Root " << *FragmentSearch.Root << "." << endl);
 
-  SetSPList(Order, FragmentSearch);
+  FragmentSearch.SetSPList(Order);
 
   // do a BFS search to fill the SP lists and label the found vertices
-  FillSPListandLabelVertices(Order, FragmentSearch, this, RestrictedKeySet);
+  FragmentSearch.FillSPListandLabelVertices(Order, RestrictedKeySet);
 
   // outputting all list for debugging
-  OutputSPList(Order, FragmentSearch);
+  FragmentSearch.OutputSPList(Order);
 
   // creating fragments with the found edge sets  (may be done in reverse order, faster)
-  int SP = CountNumbersInBondsList(Order, FragmentSearch);
+  int SP = FragmentSearch.CountNumbersInBondsList(Order);
   DoLog(0) && (Log() << Verbose(0) << "Total number of edges is " << SP << "." << endl);
   if (SP >= (Order-1)) {
@@ -804 +805 @@
 
   // free'ing the bonds lists
-  ResetSPList(Order, FragmentSearch);
+  FragmentSearch.ResetSPList(Order);
 
   // return list
@@ -856 +857 @@
   }
 
-  // initialise the fragments structure
-  FragmentSearch.FragmentCounter = 0;
-  FragmentSearch.FragmentSet = new KeySet;
-  FragmentSearch.Root = FindAtom(RootKeyNr);
-  FragmentSearch.ShortestPathList = new int[getAtomCount()];
-  for (int i=getAtomCount();i--;) {
-    FragmentSearch.ShortestPathList[i] = -1;
-  }
+  FragmentSearch.Init(FindAtom(RootKeyNr), getAtomCount());
 
   // Construct the complete KeySet which we need for topmost level only (but for all Roots)
@@ -890 +884 @@
 
       // initialise Order-dependent entries of UniqueFragments structure
-      InitialiseSPList(Order, FragmentSearch);
+      FragmentSearch.InitialiseSPList(Order);
 
       // allocate memory for all lower level orders in this 1D-array of ptrs
@@ -924 +918 @@
 
       // free Order-dependent entries of UniqueFragments structure for next loop cycle
-      FreeSPList(Order, FragmentSearch);
+      FragmentSearch.FreeSPList(Order);
     }
   }
@@ -932 +926 @@
 
   // cleanup FragmentSearch structure
-  delete[](FragmentSearch.ShortestPathList);
-  delete(FragmentSearch.FragmentSet);
+  FragmentSearch.Cleanup();
 
   // now, FragmentLowerOrdersList is complete, it looks - for BondOrder 5 - as this (number is the ANOVA Order of the terms therein)