Changes in src/Actions/FillAction/FillRegularGridAction.cpp [cae614:26b4d62]

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/Preparators/BoxFillerPreparator.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 "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"
+
 
 #include <algorithm>
@@ -79 +92 @@
   LOG(1, "INFO: Chosen molecule has " << filler->size() << " atoms.");
 
-  // center filler's tip at origin
-  filler->CenterEdge();
-
-  // prepare the filler preparator
-  BoxFillerPreparator filler_preparator(filler);
+  // check for selected molecules and create surfaces from them
+  std::vector<atom *> atoms(World::getInstance().getSelectedAtoms());
+  FillPredicate * surface_predicate = NULL;
+  LinkedCell_deprecated * LC = NULL;
+  Tesselation * TesselStruct = NULL;
   if (params.SphereRadius.get() != 0.) {
-    if (World::getInstance().beginAtomSelection() == World::getInstance().endAtomSelection()) {
+    if ( atoms.size() == 0) {
       STATUS("You have given a sphere radius "+toString(params.SphereRadius.get())
           +" != 0, but have not select any atoms.");
       return Action::failure;
     }
-    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
+    // 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
+  FillRegularGridState *UndoState = NULL;
   bool successflag = false;
-  FillRegularGridState *UndoState = NULL;
   {
+    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 = 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)) );
-        }
+    {
+      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);
+      }
     }
-    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);
-    }
+
+    // remove
+    delete mesh;
+    delete inserter;
+    delete voidnode_predicate;
+    delete surface_predicate;
+    delete LC;
+    delete TesselStruct;
   }