Changeset 7951b9 for src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

Timestamp:

Jun 13, 2012, 5:39:01 PM (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, Candidate_v1.7.0, 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:

2382d7

Parents:

e45c1d

git-author:

Frederik Heber <heber@…> (05/10/12 08:38:35)

git-committer:

Frederik Heber <heber@…> (06/13/12 17:39:01)

Message:

Rewrote SurfaceCorrelationAction such that selected atoms are used in replacement of parameter surfacemol.

• We must not request atoms or molecules inside action parameters. These must be obtained via prior selections.

File:

• src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) (2 diffs)

src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

@@ -55 +55 @@
   output.open(params.outputname.get().string().c_str());
   binoutput.open(params.binoutputname.get().string().c_str());
-  molecule *surfacemol = const_cast<molecule *>(params.Boundary.get());
-  ASSERT(surfacemol != NULL, "No molecule specified for SurfaceCorrelation.");
+
+  // check for selected molecules and create surfaces from them
+  std::vector<atom *> atoms(World::getInstance().getSelectedAtoms());
+  LinkedCell_deprecated * LCList = NULL;
+  Tesselation * TesselStruct = NULL;
   const double radius = 4.;
   double LCWidth = 20.;
@@ -65 +68 @@
       LCWidth = 2.*radius;
   }
+  if ( atoms.size() == 0) {
+    ELOG(1, "You have not select any atoms.");
+    return Action::failure;
+  }
+  // create adaptor for the selected atoms
+  PointCloudAdaptor< std::vector<atom *> > cloud(&atoms, std::string("Selected atoms"));
 
-  // get the boundary
-  class Tesselation *TesselStruct = NULL;
-  const LinkedCell_deprecated *LCList = NULL;
-  // find biggest molecule
+  // create tesselation
+  LCList = new LinkedCell_deprecated(cloud, 2.*radius);
+  TesselStruct = new Tesselation;
+  (*TesselStruct)(cloud, radius);
+
+  // correlate
   std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
   std::cout << "There are " << molecules.size() << " selected molecules." << std::endl;
-  PointCloudAdaptor<molecule> cloud(surfacemol, surfacemol->name);
-  LCList = new LinkedCell_deprecated(cloud, LCWidth);
-  FindNonConvexBorder(surfacemol, TesselStruct, LCList, radius, NULL);
   CorrelationToSurfaceMap *surfacemap = NULL;
   if (params.periodic.get())