Changeset cae614 for src/Actions/FillAction

Timestamp:

Sep 10, 2014, 7:55:12 AM (10 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:

36f45c

Parents:

a090e3

git-author:

Frederik Heber <heber@…> (09/02/14 15:06:31)

git-committer:

Frederik Heber <heber@…> (09/10/14 07:55:12)

Message:

Extracted filler preparing functionality from FillRegularGridAction.

• initialization functions placed into BaseFillerPreparator and derived BoxFillerPreparator.
• slimmed down FillRegularGridAction.
• DOCU: Extended documentation on new FillerPreparators.

File:

• src/Actions/FillAction/FillRegularGridAction.cpp (modified) (2 diffs)

src/Actions/FillAction/FillRegularGridAction.cpp

@@ -44 +44 @@
 #include "Filling/Cluster.hpp"
 #include "Filling/Filler.hpp"
-#include "Filling/Inserter/Inserter.hpp"
-#include "Filling/Inserter/RandomInserter.hpp"
-#include "Filling/Mesh/CubeMesh.hpp"
-#include "Filling/Predicates/IsInsideSurface_FillPredicate.hpp"
-#include "Filling/Predicates/IsVoidNode_FillPredicate.hpp"
-#include "Filling/Predicates/Ops_FillPredicate.hpp"
-#include "LinkedCell/linkedcell.hpp"
-#include "LinkedCell/PointCloudAdaptor.hpp"
+#include "Filling/Preparators/BoxFillerPreparator.hpp"
 #include "molecule.hpp"
 #include "MoleculeListClass.hpp"
 #include "Parser/FormatParserInterface.hpp"
 #include "Parser/FormatParserStorage.hpp"
-#include "Shapes/BaseShapes.hpp"
-#include "Tesselation/tesselation.hpp"
-#include "Tesselation/BoundaryLineSet.hpp"
-#include "Tesselation/BoundaryTriangleSet.hpp"
-#include "Tesselation/CandidateForTesselation.hpp"
 #include "World.hpp"
 
@@ -94 +82 @@
   filler->CenterEdge();
 
-  // check for selected atoms and create surfaces from them
-  std::vector<atom *> atoms(World::getInstance().getSelectedAtoms());
-  FillPredicate * surface_predicate = NULL;
-  LinkedCell_deprecated * LC = NULL;
-  Tesselation * TesselStruct = NULL;
+  // prepare the filler preparator
+  BoxFillerPreparator filler_preparator(filler);
   if (params.SphereRadius.get() != 0.) {
-    if ( atoms.size() == 0) {
+    if (World::getInstance().beginAtomSelection() == World::getInstance().endAtomSelection()) {
       STATUS("You have given a sphere radius "+toString(params.SphereRadius.get())
           +" != 0, but have not select any atoms.");
       return Action::failure;
     }
-    // create adaptor for the selected atoms
-    PointCloudAdaptor< std::vector<atom *> > cloud(&atoms, std::string("Selected atoms"));
-
-    // create tesselation
-    LC = new LinkedCell_deprecated(cloud, 2.*params.SphereRadius.get());
-    TesselStruct = new Tesselation;
-    (*TesselStruct)(cloud, params.SphereRadius.get());
-
-    // and create predicate
-    surface_predicate = new FillPredicate( IsInsideSurface_FillPredicate( *TesselStruct, *LC ) );
-  }
-
-  // create predicate, mesh, and filler
+    std::vector<atom*> atoms(World::getInstance().getSelectedAtoms());
+    filler_preparator.addSurfacePredicate(
+        params.SphereRadius.get(),
+        atoms);
+  }
+  filler_preparator.addVoidPredicate(params.mindistance.get());
+  filler_preparator.addRandomInserter(
+      params.RandAtomDisplacement.get(),
+      params.RandMoleculeDisplacement.get(),
+      params.DoRotate.get());
+  filler_preparator.addCubeMesh(
+      params.counts.get(),
+      params.offset.get(),
+      World::getInstance().getDomain().getM());
+  if (!filler_preparator()) {
+    STATUS("Filler was not fully constructed.");
+    return Action::failure;
+  }
+
+  // use filler
+  bool successflag = false;
   FillRegularGridState *UndoState = NULL;
-  bool successflag = false;
   {
-    FillPredicate *voidnode_predicate = new FillPredicate(
-        IsVoidNode_FillPredicate(
-            Sphere(zeroVec, params.mindistance.get())
-            )
-        );
-    FillPredicate Andpredicate = (*voidnode_predicate);
-    if (surface_predicate != NULL)
-      Andpredicate = (Andpredicate) && !(*surface_predicate);
-    Mesh *mesh = new CubeMesh(params.counts.get(), params.offset.get(), World::getInstance().getDomain().getM());
-    Inserter *inserter = new Inserter(
-        Inserter::impl_ptr(
-            new RandomInserter(
-                params.RandAtomDisplacement.get(),
-                params.RandMoleculeDisplacement.get(),
-                params.DoRotate.get())
-            )
-        );
-
     // fill
-    {
-      Filler *fillerFunction = new Filler(*mesh, Andpredicate, *inserter);
-      // TODO: When molecule::getBoundingSphere() does not use a sphere anymore,
-      // we need to check whether we rotate the molecule randomly. For this to
-      // work we need a sphere!
-      const Shape s = filler->getBoundingSphere(params.RandAtomDisplacement.get());
-      ClusterInterface::Cluster_impl cluster( new Cluster(filler->getAtomIds(), s) );
-      CopyAtoms_withBonds copyMethod;
-      Filler::ClusterVector_t ClonedClusters;
-      successflag = (*fillerFunction)(copyMethod, cluster, ClonedClusters);
-      delete fillerFunction;
-
-      // append each cluster's atoms to clonedatoms (however not selected ones)
-      std::vector<const atom *> clonedatoms;
-      std::vector<AtomicInfo> clonedatominfos;
-      for (Filler::ClusterVector_t::const_iterator iter = ClonedClusters.begin();
-          iter != ClonedClusters.end(); ++iter) {
-        const AtomIdSet &atoms = (*iter)->getAtomIds();
-        clonedatoms.reserve(clonedatoms.size()+atoms.size());
-        for (AtomIdSet::const_iterator atomiter = atoms.begin(); atomiter != atoms.end(); ++atomiter)
-          if (!filler->containsAtom(*atomiter)) {
-            clonedatoms.push_back( *atomiter );
-            clonedatominfos.push_back( AtomicInfo(*(*atomiter)) );
-          }
-      }
-      std::vector< BondInfo > clonedbonds;
-      StoreBondInformationFromAtoms(clonedatoms, clonedbonds);
-      LOG(2, "DEBUG: There are " << clonedatominfos.size() << " newly created atoms.");
-
-      if (!successflag) {
-        STATUS("Insertion failed, removing inserted clusters, translating original one back");
-        RemoveAtomsFromAtomicInfo(clonedatominfos);
-        clonedatoms.clear();
-        SetAtomsFromAtomicInfo(movedatoms);
-      } else {
-        std::vector<Vector> MovedToVector(filler->size(), zeroVec);
-        std::transform(filler->begin(), filler->end(), MovedToVector.begin(),
-            boost::bind(&AtomInfo::getPosition, _1) );
-        UndoState = new FillRegularGridState(clonedatominfos,clonedbonds,movedatoms,MovedToVector,params);
-      }
+    Filler *fillerFunction = filler_preparator.obtainFiller();
+    // TODO: When molecule::getBoundingSphere() does not use a sphere anymore,
+    // we need to check whether we rotate the molecule randomly. For this to
+    // work we need a sphere!
+    const Shape s = filler->getBoundingSphere(params.RandAtomDisplacement.get());
+    ClusterInterface::Cluster_impl cluster( new Cluster(filler->getAtomIds(), s) );
+    CopyAtoms_withBonds copyMethod;
+    Filler::ClusterVector_t ClonedClusters;
+    successflag = (*fillerFunction)(copyMethod, cluster, ClonedClusters);
+    delete fillerFunction;
+
+    // append each cluster's atoms to clonedatoms (however not selected ones)
+    std::vector<const atom *> clonedatoms;
+    std::vector<AtomicInfo> clonedatominfos;
+    for (Filler::ClusterVector_t::const_iterator iter = ClonedClusters.begin();
+        iter != ClonedClusters.end(); ++iter) {
+      const AtomIdSet &atoms = (*iter)->getAtomIds();
+      clonedatoms.reserve(clonedatoms.size()+atoms.size());
+      for (AtomIdSet::const_iterator atomiter = atoms.begin(); atomiter != atoms.end(); ++atomiter)
+        if (!filler->containsAtom(*atomiter)) {
+          clonedatoms.push_back( *atomiter );
+          clonedatominfos.push_back( AtomicInfo(*(*atomiter)) );
+        }
     }
-
-    // remove
-    delete mesh;
-    delete inserter;
-    delete voidnode_predicate;
-    delete surface_predicate;
-    delete LC;
-    delete TesselStruct;
+    std::vector< BondInfo > clonedbonds;
+    StoreBondInformationFromAtoms(clonedatoms, clonedbonds);
+    LOG(2, "DEBUG: There are " << clonedatominfos.size() << " newly created atoms.");
+
+    if (!successflag) {
+      STATUS("Insertion failed, removing inserted clusters, translating original one back");
+      RemoveAtomsFromAtomicInfo(clonedatominfos);
+      clonedatoms.clear();
+      SetAtomsFromAtomicInfo(movedatoms);
+    } else {
+      std::vector<Vector> MovedToVector(filler->size(), zeroVec);
+      std::transform(filler->begin(), filler->end(), MovedToVector.begin(),
+          boost::bind(&AtomInfo::getPosition, _1) );
+      UndoState = new FillRegularGridState(clonedatominfos,clonedbonds,movedatoms,MovedToVector,params);
+    }
   }