Changeset 55736b for src/Actions/FillAction

Timestamp:

Sep 15, 2014, 2:22:29 PM (11 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:

b73545

Parents:

29b35e (diff), 5a9f4c (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'Cleanup_old_code' into stable

Location:

src/Actions/FillAction

Files:

• FillRegularGridAction.cpp (modified) (2 diffs)
• FillSurfaceAction.cpp (modified) (4 diffs)
• FillSurfaceAction.def (modified) (2 diffs)
• FillVolumeAction.cpp (added)
• FillVolumeAction.def (added)
• FillVolumeAction.hpp (added)
• SuspendInMoleculeAction.cpp (added)
• SuspendInMoleculeAction.def (added)
• SuspendInMoleculeAction.hpp (added)

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"
-
 
 #include <algorithm>
@@ -92 +79 @@
   LOG(1, "INFO: Chosen molecule has " << filler->size() << " atoms.");
 
-  // 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;
+  // center filler's tip at origin
+  filler->CenterEdge();
+
+  // 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);
+    }
   }
 

src/Actions/FillAction/FillSurfaceAction.cpp ¶

@@ -46 +46 @@
 #include "Filling/Mesh/MeshAdaptor.hpp"
 #include "Filling/Predicates/IsVoidNode_FillPredicate.hpp"
+#include "Filling/Preparators/ShapeSurfaceFillerPreparator.hpp"
 #include "molecule.hpp"
 #include "Shapes/BaseShapes.hpp"
 #include "Shapes/ShapeRegistry.hpp"
+#include "Shapes/ShapeType.hpp"
 #include "World.hpp"
 
@@ -81 +83 @@
 
   // center filler's tip at origin
-  Vector max;
-  filler->CenterEdge(&max);
+  filler->CenterEdge();
 
   // determine center with respect to alignment axis
@@ -96 +97 @@
   {
     Vector translater = -1.*sum;
-    filler->Translate(&translater);
-  }
-
-  // create predicate, mesh, and filler
-  FillSurfaceState *UndoState = NULL;
-  bool successflag = false;
-  {
-    FillPredicate *voidnode_predicate = new FillPredicate(
-        IsVoidNode_FillPredicate(
-            Sphere(zeroVec, params.mindistance.get())
-            )
-        );
-
-
-    std::vector<Shape*> selectedShapes = ShapeRegistry::getInstance().getSelectedShapes();
-    if (selectedShapes.size() != 1){
-      STATUS("There has to be exactly 1 selected shape.");
+    filler->Translate(translater);
+  }
+
+  // prepare the filler preparator
+  if (ShapeRegistry::getInstance().countSelectedShapes() != (size_t)1) {
+    STATUS("Not exactly one shape selected.");
+    return Action::failure;
+  }
+  const std::vector<Shape*> shapes = ShapeRegistry::getInstance().getSelectedShapes();
+  const Shape &shape = **shapes.begin();
+
+  // hard check whether shape is of allowed type, not all are implemented
+  // but these only fail with an assertion, hence not with disable-debug
+  switch (shape.getType()) {
+    case NowhereType:
+    case EverywhereType:
+      STATUS("The shape type "+toString(shape.getType())+" is currently not supported.");
+      return Action::failure;
+      break;
+    default:
+      break;
+  }
+
+  ShapeSurfaceFillerPreparator filler_preparator(filler);
+  if (params.SphereRadius.get() != 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;
     }
-
-    boost::function<const NodeSet ()> func = 
-        boost::bind(&Shape::getHomogeneousPointsOnSurface, boost::ref(*selectedShapes[0]), params.N.get());
-    Mesh *mesh = new MeshAdaptor(func);
-    Inserter *inserter = new Inserter(
-        Inserter::impl_ptr(new SurfaceInserter(*selectedShapes[0], params.AlignedAxis.get())));
-
+    std::vector<atom*> atoms(World::getInstance().getSelectedAtoms());
+    filler_preparator.addSurfacePredicate(
+        params.SphereRadius.get(),
+        atoms);
+  }
+  filler_preparator.addVoidPredicate(params.mindistance.get());
+  filler_preparator.addSurfaceRandomInserter(
+      shape,
+      params.AlignedAxis.get(),
+      params.RandAtomDisplacement.get(),
+      params.RandMoleculeDisplacement.get());
+  filler_preparator.addShapeMesh(
+      shape,
+      params.N.get());
+  if (!filler_preparator()) {
+    STATUS("Filler was not fully constructed.");
+    return Action::failure;
+  }
+
+  // use filler
+  bool successflag = false;
+  FillSurfaceState *UndoState = NULL;
+  {
     // fill
     {
-      Filler *fillerFunction = new Filler(*mesh, *voidnode_predicate, *inserter);
+      Filler *fillerFunction = filler_preparator.obtainFiller();
       ClusterInterface::Cluster_impl cluster( new Cluster( filler->getAtomIds(), filler->getBoundingSphere() ) );
       CopyAtoms_withBonds copyMethod;
@@ -161 +189 @@
       }
     }
-
-    // remove
-    delete mesh;
-    delete inserter;
-    delete voidnode_predicate;
   }
 

src/Actions/FillAction/FillSurfaceAction.def ¶

@@ -20 +20 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (unsigned int)(double)(Vector)
-#define paramtokens ("count")("min-distance")("Alignment-Axis")
-#define paramdescriptions ("number of instances to be added, changed according to geometric needs")("minimum distance between added instances")("The filler molecule is rotated relative to this alignment axis")
-#define paramdefaults (PARAM_DEFAULT(12))(PARAM_DEFAULT(1.))(NOPARAM_DEFAULT)
-#define paramreferences (N)(mindistance)(AlignedAxis)
+#define paramtypes (unsigned int)(double)(double)(double)(double)(Vector)
+#define paramtokens ("count")("min-distance")("tesselation-radius")("random-atom-displacement")("random-molecule-displacement")("Alignment-Axis")
+#define paramdescriptions ("number of instances to be added, changed according to geometric needs")("minimum distance between added instances")("radius of rolling sphere in tesselating selected molecule's surfaces")("magnitude of random atom displacement")("magnitude of random molecule displacement")("The filler molecule is rotated relative to this alignment axis")
+#define paramdefaults (PARAM_DEFAULT(12))(PARAM_DEFAULT(1.))(PARAM_DEFAULT(0.))(PARAM_DEFAULT(0.))(PARAM_DEFAULT(0.))(NOPARAM_DEFAULT)
+#define paramreferences (N)(mindistance)(SphereRadius)(RandAtomDisplacement)(RandMoleculeDisplacement)(AlignedAxis)
 #define paramvalids \
 (DummyValidator< unsigned int >()) \
+(BoxLengthValidator()) \
+(BoxLengthValidator()) \
+(BoxLengthValidator()) \
 (BoxLengthValidator()) \
 (VectorNotZeroValidator())
@@ -36 +39 @@
 #define CATEGORY Fill
 #define MENUNAME "fill"
-#define MENUPOSITION 1
+#define MENUPOSITION 2
 #define ACTIONNAME Surface
 #define TOKEN "fill-surface"