Changeset c7c615 for src/Actions/FragmentationAction

Timestamp:

Feb 27, 2013, 12:42:36 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, 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:

9291d04

Parents:

1edc87

git-author:

Frederik Heber <heber@…> (12/11/12 10:37:58)

git-committer:

Frederik Heber <heber@…> (02/27/13 12:42:36)

Message:

FIX: FragmentationAction gave wrong number of molecules.

File:

• src/Actions/FragmentationAction/FragmentationAction.cpp (modified) (4 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -36 +36 @@
 
 #include "Atom/atom.hpp"
+#include "CodePatterns/IteratorAdaptors.hpp"
 #include "CodePatterns/Log.hpp"
 #include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
@@ -47 +48 @@
 #include "World.hpp"
 
+#include <boost/shared_ptr.hpp>
 #include <boost/filesystem.hpp>
+#include <algorithm>
 #include <iostream>
 #include <map>
@@ -89 +92 @@
     atomids.push_back(iter->second->getId());
   }
-  LOG(1, "INFO: There are " << clusters.size()  << " molecules to consider.");
+  {
+    std::vector<molecule *> molecules;
+    molecules.insert( molecules.end(), MapKeyIterator<clusters_t::const_iterator>(clusters.begin()),
+        MapKeyIterator<clusters_t::const_iterator>(clusters.end()) );
+    molecules.erase( std::unique(molecules.begin(), molecules.end()), molecules.end() );
+    LOG(1, "INFO: There are " << molecules.size()  << " molecules to consider.");
+  }
 
   // get whether to saturate or not
@@ -134 +143 @@
     LOG(2, "INFO: Fragmenting in molecule " << mol->getName() << " in " << clusters.count(mol) 
         << " atoms, out of " << mol->getAtomCount() << ".");
-    const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
     Fragmentation Fragmenter(mol, *FileChecker, saturation);