Changeset f10b0c for src/Actions/FragmentationAction

Timestamp:

Jun 11, 2012, 9:53:19 AM (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, 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:

95f965

Parents:

b9c69d

git-author:

Michael Ankele <ankele@…> (04/24/12 13:55:16)

git-committer:

Frederik Heber <heber@…> (06/11/12 09:53:19)

Message:

disastrously big and ugly commit

• using new Parameter<T> classes:
  • Actions
  • Queries (all UIs)

• TODO:
  • actions crash cause Value is unset
  • no query<BoxVector>

File:

• src/Actions/FragmentationAction/FragmentationAction.cpp (modified) (2 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -45 +45 @@
 
   LOG(0, "STATUS: Fragmenting molecular system with current connection matrix maximum bond distance "
-      << params.distance << " up to "
-      << params.order << " order. Fragment files begin with "
-      << params.prefix << " and are stored as: "
-      << params.types << "." << std::endl);
+      << params.distance.get() << " up to "
+      << params.order.get() << " order. Fragment files begin with "
+      << params.prefix.get() << " and are stored as: "
+      << params.types.get() << "." << std::endl);
 
   DepthFirstSearchAnalysis DFS;
@@ -54 +54 @@
     mol = iter->second;
     ASSERT(mol != NULL, "No molecule has been picked for fragmentation.");
-    LOG(2, "INFO: Fragmenting molecule with bond distance " << params.distance << " angstroem, order of " << params.order << ".");
+    LOG(2, "INFO: Fragmenting molecule with bond distance " << params.distance.get() << " angstroem, order of " << params.order.get() << ".");
     start = clock();
     if (mol->hasBondStructure()) {
-      Fragmentation Fragmenter(mol, params.DoSaturation ? DoSaturate : DontSaturate);
-      Fragmenter.setOutputTypes(params.types);
-      ExitFlag = Fragmenter.FragmentMolecule(params.order, params.prefix, DFS);
+      Fragmentation Fragmenter(mol, params.DoSaturation.get() ? DoSaturate : DontSaturate);
+      Fragmenter.setOutputTypes(params.types.get());
+      ExitFlag = Fragmenter.FragmentMolecule(params.order.get(), params.prefix.get(), DFS);
     }
     World::getInstance().setExitFlag(ExitFlag);