Changeset 06f41f3 for src/Fragmentation

Timestamp:

Dec 3, 2012, 9:49:30 AM (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:

9511c7

Parents:

b78dfd

git-author:

Frederik Heber <heber@…> (09/19/12 13:55:43)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:49:30)

Message:

CheckAgainstAdjacencyFile now works on given vector of atomids.

• added helper function getGlobalIdsFromLocalIds() as we have to translate molecule's internal ids to global atomId_t to check against those in file.
• TESTFIX: Adapted CheckAgainstAdjacencyFileUnitTest to the changes, also added another test case to operatorTest().

Location:

src/Fragmentation

Files:

• Fragmentation.cpp (modified) (2 diffs)
• fragmentation_helpers.cpp (modified) (1 diff)

src/Fragmentation/Fragmentation.cpp

@@ -49 +49 @@
 #include "Fragmentation/fragmentation_helpers.hpp"
 #include "Fragmentation/Graph.hpp"
+#include "Fragmentation/helpers.hpp"
 #include "Fragmentation/KeySet.hpp"
 #include "Fragmentation/PowerSetGenerator.hpp"
@@ -137 +138 @@
 
     CheckAgainstAdjacencyFile FileChecker(File);
-    FragmentationToDo = FragmentationToDo && FileChecker(World::getInstance().beginAtomSelection(), World::getInstance().endAtomSelection());
+    const std::vector<atomId_t> globalids = getGlobalIdsFromLocalIds(*mol, atomids);
+    FragmentationToDo = FragmentationToDo && FileChecker(globalids);
   }
 

src/Fragmentation/fragmentation_helpers.cpp

@@ -151 +151 @@
   std::vector<atomId_t> globalids;
   globalids.reserve(atomids.size());
-  const AtomIdSet &mol_ids = mol.getAtomIds();
   BOOST_FOREACH( atomId_t id, atomids ) {
-    AtomIdSet::const_iterator iter = mol_ids.find(id);
+    molecule::const_iterator iter = mol.begin();
+    for (; iter != mol.end(); ++iter) {
+      if ( (*iter)->getNr() == (int)id)
+        break;
+    }
     ASSERT( iter != mol.end(),
-        "getGlobalFromLocal() - could not find id "+toString(id)
+        "getGlobalIdsFromLocalIds() - could not find id "+toString(id)
         +" in molecule "+toString(mol.getName()));
     globalids.push_back( (*iter)->getId() );