Changeset d760bb for src/Fragmentation/fragmentation_helpers.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_helpers.cpp (modified) (5 diffs)

src/Fragmentation/fragmentation_helpers.cpp

@@ -37 +37 @@
 #include "fragmentation_helpers.hpp"
 
+#include <algorithm>
 #include <sstream>
 
+#include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
 
 #include "Atom/atom.hpp"
-#include "Bond/bond.hpp"
-#include "Element/element.hpp"
 #include "Fragmentation/AdaptivityMap.hpp"
 #include "Fragmentation/AtomMask.hpp"
@@ -82 +82 @@
  * \param *mol molecule with atoms and bonds
  */
-int CombineAllOrderListIntoOne(Graph &FragmentList, Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
+int CombineAllOrderListIntoOne(Graph &FragmentList, std::vector<Graph*> *&FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
 {
   int RootNr = 0;
@@ -99 +99 @@
     RootStack.pop_front();
     Walker = mol->FindAtom(RootKeyNr);
-    NumLevels = 1 << (Walker->AdaptiveOrder - 1);
+    NumLevels = Walker->AdaptiveOrder;
+    ASSERT( NumLevels == FragmentLowerOrdersList[RootNr].size(),
+        "CombineAllOrderListIntoOne() - differing size and NumLevels.");
     for(int i=0;i<NumLevels;i++) {
       if (FragmentLowerOrdersList[RootNr][i] != NULL) {
@@ -113 +115 @@
 /** Free's memory allocated for all KeySets from all orders.
  * \param *out output stream for debugging
- * \param ***FragmentLowerOrdersList
+ * \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)
+void FreeAllOrdersList(std::vector<Graph*> *&FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
 {
   LOG(1, "Free'ing the lists of all orders per order.");
@@ -128 +130 @@
     RootStack.pop_front();
     Walker = mol->FindAtom(RootKeyNr);
-    NumLevels = 1 << (Walker->AdaptiveOrder - 1);
+    NumLevels = Walker->AdaptiveOrder;
     for(int i=0;i<NumLevels;i++) {
       if (FragmentLowerOrdersList[RootNr][i] != NULL) {
-        delete(FragmentLowerOrdersList[RootNr][i]);
+        delete FragmentLowerOrdersList[RootNr][i];
       }
+      FragmentLowerOrdersList[RootNr].clear();
     }
-    delete[](FragmentLowerOrdersList[RootNr]);
     RootNr++;
   }
-  delete[](FragmentLowerOrdersList);
+  delete[] FragmentLowerOrdersList;
 };