Changeset f10b0c for src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

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/MoleculeAction/FillWithMoleculeAction.cpp (modified) (3 diffs)

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -46 +46 @@
 
   LOG(1, "INFO: Filling Box with water molecules, "
-      << " minimum distance to molecules" << params.boundary
-      << ", random atom displacement " << params.RandAtomDisplacement
-      << ", random molecule displacement " << params.RandMoleculeDisplacement
-      << ", distances between fillers (" << params.distances[0] << "," << params.distances[1] << "," << params.distances[2]
-      << "), MinDistance " << params.MaxDistance
-      << ", DoRotate " << params.DoRotate << ".");
+      << " minimum distance to molecules" << params.boundary.get()
+      << ", random atom displacement " << params.RandAtomDisplacement.get()
+      << ", random molecule displacement " << params.RandMoleculeDisplacement.get()
+      << ", distances between fillers (" << params.distances.get()[0] << "," << params.distances.get()[1] << "," << params.distances.get()[2]
+      << "), MinDistance " << params.MaxDistance.get()
+      << ", DoRotate " << params.DoRotate.get() << ".");
   // construct water molecule
   std::vector<molecule *> presentmolecules = World::getInstance().getAllMolecules();
 //  LOG(0, presentmolecules.size() << " molecules initially are present.");
-  std::string FilenameSuffix = params.fillername.string().substr(params.fillername.string().find_last_of('.')+1, params.fillername.string().length());
+  std::string FilenameSuffix = params.fillername.get().string().substr(params.fillername.get().string().find_last_of('.')+1, params.fillername.get().string().length());
   ifstream input;
-  LOG(0, "STATUS: Loading filler molecule " << params.fillername.string().c_str()
+  LOG(0, "STATUS: Loading filler molecule " << params.fillername.get().string().c_str()
       << " of suffix " << FilenameSuffix << ".");
-  input.open(params.fillername.string().c_str());
+  input.open(params.fillername.get().string().c_str());
   FormatParserStorage::getInstance().load(input, FilenameSuffix);
   input.close();
@@ -67 +67 @@
   ASSERT(filler != NULL,
       "MoleculeFillWithMoleculeAction::performCall() - no last molecule found, nothing parsed?.");
-  filler->SetNameFromFilename(params.fillername.string().c_str());
+  filler->SetNameFromFilename(params.fillername.get().string().c_str());
   World::AtomComposite Set = filler->getAtomSet();
   LOG(1, "INFO: The filler molecules has " << Set.size() << " atoms.");
@@ -78 +78 @@
   double distance[NDIM];
   for (int i=0;i<NDIM;i++)
-    distance[i] = params.distances[i];
+    distance[i] = params.distances.get()[i];
   FillBoxWithMolecule(
       World::getInstance().getMolecules(),
       filler, *(World::getInstance().getConfig()),
-      params.MaxDistance,
+      params.MaxDistance.get(),
       distance,
-      params.boundary,
-      params.RandAtomDisplacement,
-      params.RandMoleculeDisplacement,
-      params.DoRotate);
+      params.boundary.get(),
+      params.RandAtomDisplacement.get(),
+      params.RandMoleculeDisplacement.get(),
+      params.DoRotate.get());
   for (molecule::iterator iter = filler->begin(); !filler->empty(); iter = filler->begin()) {
     atom *Walker = *iter;