Changeset 13c5c1 for src/Actions/FragmentationAction/FragmentationAction.cpp

Timestamp:

Aug 9, 2013, 2:20:38 PM (12 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, Candidate_v1.7.1, 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:

cd9a59

Parents:

0331ee

git-author:

Frederik Heber <heber@…> (07/05/13 08:52:38)

git-committer:

Frederik Heber <heber@…> (08/09/13 14:20:38)

Message:

FragmentationAction uses Interfragmenter to add non-bonded fragments.

File:

• src/Actions/FragmentationAction/FragmentationAction.cpp (modified) (3 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -47 +47 @@
 #include "Fragmentation/Graph.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
+#include "Fragmentation/Interfragmenter.hpp"
 #include "Graph/AdjacencyList.hpp"
 #include "Graph/BondGraph.hpp"
@@ -76 +77 @@
 
   // inform about used parameters
-  LOG(0, "STATUS: Fragmenting molecular system with current connection matrix maximum bond distance "
-      << params.distance.get() << " up to "
+  LOG(0, "STATUS: Fragmenting molecular system with current connection matrix up to "
       << params.order.get() << " order. ");
   if (params.types.get().size() != 0)
@@ -176 +176 @@
   }
   LOG(0, "STATUS: There are " << TotalGraph.size() << " fragments.");
+
+  // now add interfragments
+  if (params.InterOrder.get() != 0) {
+    LOG(0, "STATUS: Putting fragments together up to order "
+        << params.InterOrder.get() << " and distance of "
+        << params.distance.get() << ".");
+    Interfragmenter fragmenter(TotalGraph);
+    const enum HydrogenTreatment treatment =  params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
+    fragmenter(params.InterOrder.get(), params.distance.get(), treatment);
+    LOG(0, "STATUS: There are now " << TotalGraph.size() << " fragments after interfragmenting.");
+  }
 
   // store keysets to file