Changeset d760bb for src/Fragmentation/Fragmentation.cpp

Timestamp:

Feb 24, 2013, 12:59:18 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, Candidate_v1.7.0, 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:

c91572

Parents:

b6b5b8

git-author:

Frederik Heber <heber@…> (02/19/13 12:42:38)

git-committer:

Frederik Heber <heber@…> (02/24/13 12:59:18)

Message:

REFACTOR: PowerSetGenerator now creates all orders in one go, not limited to one by one increments.

• atom_bondedparticle's MaxOrder is not a bool but an int containing the desired final order set by CheckOrderAtSite and compared to AdaptiveOrder to obtain its old meaning.
• UniqueFragments now contains a vector of n Graphs to place n-body fragments in that are later combined. Also, cleaned up a lot of old functions and merged stuff into cstor. FreeAllOrdersList() and CombineAllOrderListIntoOne() have been adapted accordingly.
• Fragmentation::FragmentBOSSANOVA now uses fully again FragmentLowerOrdersList which now has the above n slots to place n-body fragments in and which is passed by ref to UniqueFragments.
• SPFragmentGenerator now always stores the current fragment, only in a specific slot in UniqueFragment's Graphs, and it recurses if there are enough SP levels and plces left.
• FIX: BondsPerShortestPath properly prints and informs about resetting the path list.
• We checked extra that BondFragments come out exactly as before (same order because of the Graph being a map naturally). The only difference is the OrderAtSite file which now has more than 0/1 values in the second entry.

File:

• src/Fragmentation/Fragmentation.cpp (modified) (7 diffs)

src/Fragmentation/Fragmentation.cpp

@@ -200 +200 @@
 {
   Info FunctionInfo(__func__);
-  Graph ***FragmentLowerOrdersList = NULL;
+  std::vector<Graph*> *FragmentLowerOrdersList = NULL;
   int NumLevels = 0;
   int NumMolecules = 0;
@@ -210 +210 @@
   int RootKeyNr = 0;
   int RootNr = 0;
-  UniqueFragments FragmentSearch;
 
   // FragmentLowerOrdersList is a 2D-array of pointer to MoleculeListClass objects, one dimension represents the ANOVA expansion of a single order (i.e. 5)
   // with all needed lower orders that are subtracted, the other dimension is the BondOrder (i.e. from 1 to 5)
   NumMoleculesOfOrder = new int[UpgradeCount];
-  FragmentLowerOrdersList = new Graph**[UpgradeCount];
-
-  for(int i=0;i<UpgradeCount;i++) {
+  FragmentLowerOrdersList = new std::vector<Graph*>[UpgradeCount];
+
+  for(int i=0;i<UpgradeCount;i++)
     NumMoleculesOfOrder[i] = 0;
-    FragmentLowerOrdersList[i] = NULL;
-  }
-
-  FragmentSearch.Init(mol->FindAtom(RootKeyNr));
 
   // Construct the complete KeySet which we need for topmost level only (but for all Roots)
@@ -244 +239 @@
     //} else
     {
-      // increase adaptive order by one
-      Walker->GetTrueFather()->AdaptiveOrder++;
+      // set adaptive order to desired max order
+      Walker->GetTrueFather()->AdaptiveOrder = Walker->GetTrueFather()->MaxOrder;
       Order = Walker->AdaptiveOrder = Walker->GetTrueFather()->AdaptiveOrder;
 
+      // allocate memory for all lower level orders
+      NumLevels = Order;
+      FragmentLowerOrdersList[RootNr].resize(NumLevels, NULL);
+      for( size_t i=0;i<NumLevels;++i)
+        FragmentLowerOrdersList[RootNr][i] = new Graph;
+
       // initialise Order-dependent entries of UniqueFragments structure
-      class PowerSetGenerator PSG(&FragmentSearch, Walker->AdaptiveOrder);
-
-      // allocate memory for all lower level orders in this 1D-array of ptrs
-      NumLevels = 1 << (Order-1); // (int)pow(2,Order);
-      FragmentLowerOrdersList[RootNr] = new Graph*[NumLevels];
-      for (int i=0;i<NumLevels;i++)
-        FragmentLowerOrdersList[RootNr][i] = NULL;
+      UniqueFragments FragmentSearch(1., FragmentLowerOrdersList[RootNr], Walker);
+      PowerSetGenerator PSG(&FragmentSearch, Walker->AdaptiveOrder);
 
       // create top order where nothing is reduced
       LOG(0, "==============================================================================================================");
-      LOG(0, "Creating KeySets of Bond Order " << Order << " for " << *Walker << ", " << (RootStack.size()-RootNr) << " Roots remaining."); // , NumLevels is " << NumLevels << "
+      LOG(0, "Creating KeySets up till Bond Order " << Order << " for " << *Walker << ", " << (RootStack.size()-RootNr) << " Roots remaining."); // , NumLevels is " << NumLevels << "
 
       // Create list of Graphs of current Bond Order (i.e. F_{ij})
-      FragmentLowerOrdersList[RootNr][0] = new Graph;
-      FragmentSearch.PrepareForPowersetGeneration(1., FragmentLowerOrdersList[RootNr][0], Walker);
       NumMoleculesOfOrder[RootNr] = PSG(CompleteMolecule, saturation);
 
@@ -270 +264 @@
       if (NumMoleculesOfOrder[RootNr] != 0) {
         NumMolecules = 0;
-      } else {
-        Walker->GetTrueFather()->MaxOrder = true;
       }
       // now, we have completely filled each cell of FragmentLowerOrdersList[] for the current Walker->AdaptiveOrder
@@ -284 +276 @@
   LOG(1, "Total number of resulting molecules is: " << TotalNumMolecules << ".");
   LOG(0, "==============================================================================================================");
-
-  // cleanup FragmentSearch structure
-  FragmentSearch.Cleanup();
 
   // now, FragmentLowerOrdersList is complete, it looks - for BondOrder 5 - as this (number is the ANOVA Order of the terms therein)
@@ -362 +351 @@
     delete[](IndexKeySetList);
   } else { // global increase of Bond Order
-    for(molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+    for(molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
       if (AtomMask.isTrue((*iter)->getNr())) { // skip masked out
+        (*iter)->MaxOrder = (Order != 0 ? Order : (*iter)->MaxOrder+1);
         // remove all that have reached desired order
-        if ((Order != 0) && ((*iter)->AdaptiveOrder >= Order)) // && ((*iter)->AdaptiveOrder < MinimumRingSize[(*iter)->getNr()]))
+        if ((*iter)->AdaptiveOrder >= (*iter)->MaxOrder) // && ((*iter)->AdaptiveOrder < MinimumRingSize[(*iter)->getNr()]))
           AtomMask.setFalse((*iter)->getNr());
         else
@@ -450 +440 @@
     for(molecule::iterator iter=mol->begin();iter!=mol->end();++iter){
       (*iter)->AdaptiveOrder = OrderArray[(*iter)->getNr()];
-      (*iter)->MaxOrder = MaxArray.isTrue((*iter)->getNr());
+      (*iter)->MaxOrder = OrderArray[(*iter)->getNr()]; //MaxArray.isTrue((*iter)->getNr());
     }
     //SetAtomValueToIndexedArray( OrderArray, &atom::getNr(), &atom::AdaptiveOrder );