Changeset e65878 for src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp

Timestamp:

Oct 31, 2011, 11:49:19 AM (14 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:

870b4b

Parents:

505d05

git-author:

Frederik Heber <heber@…> (05/18/11 19:55:05)

git-committer:

Frederik Heber <heber@…> (10/31/11 11:49:19)

Message:

Selection is now done inside DipoleAngularCorrelation.

• as molecules may change over time it makes more sense to select molecules internally right now.
• DipoleAngularCorrelation() now takes Formula instead of std::vector<atom *>.
• also adjusted const'ness of some parameters.

File:

• src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) (3 diffs)

src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp

@@ -24 +24 @@
 #include "linkedcell.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Descriptors/AtomOfMoleculeSelectionDescriptor.hpp"
+#include "Descriptors/MoleculeFormulaDescriptor.hpp"
 #include "Element/element.hpp"
-#include "molecule.hpp"
 #include "Element/periodentafel.hpp"
 #include "LinearAlgebra/Vector.hpp"
+#include "molecule.hpp"
 #include "World.hpp"
 #include "WorldTime.hpp"
@@ -53 +55 @@
 
   // get selected atoms
-  std::vector<atom*> atoms = World::getInstance().getSelectedAtoms();
-  ASSERT(atoms.size() != 0, "AnalysisDipoleAngularCorrelationAction() - not atoms selected.");
+  std::vector<atom*> old_atom_selection = World::getInstance().getSelectedAtoms();
+  std::vector<molecule*> old_molecule_selection = World::getInstance().getSelectedMolecules();
 
   // get current time step
   const unsigned int oldtime = WorldTime::getTime();
 
-  // obtain zero dipole orientation
+  // select atoms and obtain zero dipole orientation
+  Formula DipoleFormula(params.DipoleFormula);
   World::getInstance().setTime(0);
-  std::map<atomId_t, Vector> ZeroVector = CalculateZeroAngularDipole(atoms);
+  World::getInstance().clearMoleculeSelection(); // TODO: This should be done in setTime or where molecules are re-done
+  World::getInstance().selectAllMolecules(MoleculeByFormula(DipoleFormula));
+  std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
+  std::map<atomId_t, Vector> ZeroVector = CalculateZeroAngularDipole(molecules);
 
   // go through each step of common trajectory of all atoms in set
+  World::getInstance().clearAtomSelection();
+  World::getInstance().selectAllAtoms(AtomsByMoleculeSelection());
+  std::vector<atom *> atoms = World::getInstance().getSelectedAtoms();
   range<size_t> timesteps = getMaximumTrajectoryBounds(atoms);
   for (size_t step = 0; step < timesteps.first; ++step) {
     // calculate dipoles relative to zero orientation
     DipoleAngularCorrelationMap *correlationmap = NULL;
-    correlationmap = DipoleAngularCorrelation(atoms, step, ZeroVector, DontResetTime);
+    correlationmap = DipoleAngularCorrelation(DipoleFormula, step, ZeroVector, DontResetTime);
 
     // prepare step string in filename
@@ -102 +111 @@
   World::getInstance().setTime(oldtime);
 
+  // reset to old selections
+  World::getInstance().clearAtomSelection();
+  BOOST_FOREACH(atom *_atom, old_atom_selection) {
+    World::getInstance().selectAtom(_atom);
+  }
+  World::getInstance().clearMoleculeSelection();
+  BOOST_FOREACH(molecule *_mol, old_molecule_selection) {
+    World::getInstance().selectMolecule(_mol);
+  }
+
   // exit
   return Action::success;