Changeset d760bb for src/Fragmentation/UniqueFragments.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/UniqueFragments.cpp (modified) (6 diffs)

src/Fragmentation/UniqueFragments.cpp

@@ -37 +37 @@
 #include "UniqueFragments.hpp"
 
+#include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
 
@@ -48 +49 @@
 /** Constructor of class UniqueFragments.
  *
+ * @param _TEFactor total energy factor
+ * @param _Leaflet current graph to work on
+ * @param _Root root atom
  */
-UniqueFragments::UniqueFragments()
-{}
+UniqueFragments::UniqueFragments(double _TEFactor, std::vector<Graph*> &_Leaflets, atom *_Root) :
+    FragmentCounter(0),
+    Root(_Root),
+    TEFactor(_TEFactor),
+    Leaflets(_Leaflets)
+{
+  FragmentSet = new KeySet;
+}
 
 /** Destructor of class UniqueFragments.
@@ -56 +66 @@
  */
 UniqueFragments::~UniqueFragments()
-{}
+{
+  Cleanup();
+}
 
 /** Checking whether KeySet is not already present in Graph, if so just adds factor.
+ *
+ * \param order order at which to insert
  */
-void UniqueFragments::InsertFragmentIntoGraph()
+void UniqueFragments::InsertFragmentIntoGraph(const size_t order)
 {
   GraphTestPair testGraphInsert;
 
-  testGraphInsert = Leaflet->insert(GraphPair (*FragmentSet,std::pair<int,double>(FragmentCounter,TEFactor)));  // store fragment number and current factor
+  ASSERT( Leaflets.size() > order,
+      "UniqueFragments::InsertFragmentIntoGraph() - Leaflets has only "
+      +toString(Leaflets.size())+" entries, not enough for "+toString(order));
+  testGraphInsert = Leaflets[order]->insert(GraphPair (*FragmentSet,std::pair<int,double>(FragmentCounter,TEFactor)));  // store fragment number and current factor
   if (testGraphInsert.second) {
     LOG(2, "KeySet " << FragmentCounter << " successfully inserted.");
@@ -75 +92 @@
 };
 
-/** Initialization for UniqueFragments.
- *
- * \param _Root ref to atom to start from (with graph algorithms, hence root node)
- * \param AtomCount number of nodes/atoms
- */
-void UniqueFragments::Init(atom *_Root)
-{
-  // initialise the fragments structure
-  FragmentCounter = 0;
-  FragmentSet = new KeySet;
-  Root = _Root;
-}
-
 /** Removes some allocated memory.
  *
@@ -93 +97 @@
 void UniqueFragments::Cleanup()
 {
-  delete(FragmentSet);
+  delete FragmentSet;
 }
 
@@ -113 +117 @@
   Root=_root;
 }
-
-/** Sets initial values before PowerSetGenerator uses this class.
- *
- * @param _TEFactor total energy factor
- * @param _Leaflet current graph to work on
- * @param _Root root atom
- */
-void UniqueFragments::PrepareForPowersetGeneration(double _TEFactor, Graph *_Leaflet, atom *_Root)
-{
-  TEFactor = _TEFactor;
-  Leaflet = _Leaflet;
-  Root = _Root;
-}