Changeset b1c5f46

Timestamp:

Oct 13, 2015, 8:14:32 PM (9 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:

cee9e8

Parents:

0d9053

git-author:

Frederik Heber <heber@…> (09/01/15 13:46:05)

git-committer:

Frederik Heber <heber@…> (10/13/15 20:14:32)

Message:

Interfragmenter now combines two fragments up to (in sum) till MaxOrder.

• before only fragments of each MaxOrder were allowed, now the sum of their bond order must not exceed maxOrder, i.e. MaxOrder of 4 means 1+1, 1+2, 1+3, 2+2, 3+1, 2+1, 1+1 (with order of left and right fragment that are joined).

Location:

src/Fragmentation

Files:

• Interfragmenter.cpp (modified) (4 diffs)
• Interfragmenter.hpp (modified) (1 diff)

src/Fragmentation/Interfragmenter.cpp

@@ -154 +154 @@
 
 void Interfragmenter::combineFragments(
+    const size_t _MaxOrder,
     const candidates_t &_candidates,
     atomkeyset_t &_fragmentmap,
@@ -169 +170 @@
         +toString(_atom->getId())+" in fragment specific lookup.");
     keysets_t &othersets = finditer->second;
+    ASSERT( !othersets.empty(),
+        "Interfragmenter::combineFragments() - keysets to "+toString(_atom->getId())+
+        "is empty.");
     keysets_t::iterator otheriter = othersets.begin();
     while (otheriter != othersets.end()) {
@@ -175 +179 @@
       // only add them one way round and not the other
       if (otherset < _keyset) {
+        ++otheriter;
+        continue;
+      }
+      // only add if combined they don't exceed the desired maxorder
+      if (otherset.size() + _keyset.size() > _MaxOrder) {
+        LOG(3, "INFO: Rejecting " << otherset << " as in sum their orders exceed " << _MaxOrder);
         ++otheriter;
         continue;
@@ -217 +227 @@
     /// combine each remaining fragment with current fragment to a new fragment
     /// if keyset is less (to prevent addding same inter-fragment twice)
-    combineFragments(candidates, fragmentmap, keyset, InterFragments, counter);
+    combineFragments(MaxOrder, candidates, fragmentmap, keyset, InterFragments, counter);
   }
 

src/Fragmentation/Interfragmenter.hpp

@@ -111 +111 @@
    */
   void combineFragments(
+      const size_t _MaxOrder,
       const candidates_t &_candidates,
       atomkeyset_t &_fragmentmap,