Changeset 901d87

Timestamp:

Mar 30, 2012, 9:18:26 AM (13 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:

f61f61

Parents:

dba7b0

git-author:

Frederik Heber <heber@…> (02/21/12 13:27:44)

git-committer:

Frederik Heber <heber@…> (03/30/12 09:18:26)

Message:

Refactored insertion of cluster into Inserter class.

• this is to allow for random variations and alike with arbitrary inserters.
• Filler now requires an Inserter in cstor which is used when placing a cluster at a specific node.
• the Inserter::operator() uses CopyAtomsInterface to pass on to Cluster::clone().
• FillRegularGridAction uses SimpleInserter now.
• TESTFIX: FillerUnitTest uses SimpleInserter, too, now.

Location:

src

Files:

• Actions/FillAction/FillRegularGridAction.cpp (modified) (2 diffs)
• Filling/Filler.cpp (modified) (3 diffs)
• Filling/Filler.hpp (modified) (3 diffs)
• Filling/Inserter/Inserter.hpp (added)
• Filling/Inserter/SimpleInserter.cpp (added)
• Filling/Inserter/SimpleInserter.hpp (added)
• Filling/Makefile.am (modified) (2 diffs)
• Filling/unittests/FillerUnitTest.cpp (modified) (3 diffs)
• Filling/unittests/FillerUnitTest.hpp (modified) (2 diffs)

src/Actions/FillAction/FillRegularGridAction.cpp

@@ -26 +26 @@
 #include "Filling/Cluster.hpp"
 #include "Filling/Filler.hpp"
+#include "Filling/Inserter/SimpleInserter.hpp"
 #include "Filling/Mesh/CubeMesh.hpp"
 #include "Filling/Predicates/IsInsideSurface_FillPredicate.hpp"
@@ -111 +112 @@
     // fill
     {
-      Filler *fillerFunction = new Filler(*mesh, Andpredicate);
+      SimpleInserter inserter;
+      Filler *fillerFunction = new Filler(*mesh, Andpredicate, inserter);
       ClusterInterface::Cluster_impl cluster( new Cluster( filler->getAtomIds(), filler->getBoundingShape()) );
       CopyAtoms_withBonds copyMethod;

src/Filling/Filler.cpp

@@ -35 +35 @@
 #include "ClusterInterface.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
+#include "Inserter/Inserter.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "NodeTypes.hpp"
@@ -47 +48 @@
  * remove_copy_if which works in this inverted way as desired.
  *
- * @param mesh Mesh with a NodeSet that fills its Shape
- * @param predicate predicate construct to check at each Node
+ * @param _mesh Mesh with a NodeSet that fills its Shape
+ * @param _predicate predicate construct to check at each Node
+ * @param _inserter inserter which places the cloned cluster
  */
-Filler::Filler(const Mesh &_mesh, const FillPredicate &_predicate) :
+Filler::Filler(const Mesh &_mesh, const FillPredicate &_predicate, const Inserter &_inserter) :
   mesh(_mesh),
-  predicate(!_predicate)
+  predicate(!_predicate),
+  inserter(_inserter)
 {}
 
@@ -100 +103 @@
   // fill all other true nodes
   std::for_each(iter , FillNodes.end(),
-      boost::bind(&ClusterInterface::clone, boost::cref(cluster), boost::ref(copyMethod), _1) );
+      boost::bind(&Inserter::operator(), boost::cref(inserter), boost::ref(copyMethod), boost::cref(cluster), _1) );
 
   // move cluster to first node

src/Filling/Filler.hpp

@@ -22 +22 @@
 class CopyAtomsInterface;
 class FillPredicate;
+class Inserter;
 class Mesh;
 
@@ -31 +32 @@
 {
 public:
-  Filler(const Mesh &_mesh, const FillPredicate &_predicate);
+  Filler(const Mesh &_mesh, const FillPredicate &_predicate, const Inserter &_inserter);
   ~Filler();
 
@@ -41 +42 @@
   //!> the predicate is evaluted whether a Node in the NodeSet of mesh is filled or not
   const FillPredicate predicate;
-
+  //!> Inserter function to allow for some changes when placing the cluster at the node
+  const Inserter &inserter;
 };
 

src/Filling/Makefile.am

@@ -8 +8 @@
         Filling/Filler.cpp \
         Filling/Generators/NodeGenerator.cpp \
+        Filling/Inserter/SimpleInserter.cpp \
         Filling/Predicates/AnyFillPredicate.cpp \
         Filling/Predicates/FillPredicate.cpp \
@@ -22 +23 @@
         Filling/Filler.hpp \
         Filling/Generators/NodeGenerator.hpp \
+        Filling/Inserter/Inserter.hpp \
+        Filling/Inserter/SimpleInserter.hpp \
         Filling/NodeTypes.hpp \
         Filling/Predicates/AnyFillPredicate.hpp \

src/Filling/unittests/FillerUnitTest.cpp

@@ -30 +30 @@
 #include "Filling/Cluster.hpp"
 #include "Filling/Filler.hpp"
+#include "Filling/Inserter/SimpleInserter.hpp"
 #include "Filling/Mesh/Mesh.hpp"
 #include "Filling/Predicates/FillPredicate.hpp"
@@ -70 +71 @@
   predicate = new FillPredicate(AlwaysFillPredicate());
   mesh = new MeshStub();
+  inserter = new SimpleInserter();
   CPPUNIT_ASSERT_EQUAL( (size_t)5, mesh->getNodes().size() );
-  filler = new Filler(*mesh, *predicate);
+  filler = new Filler(*mesh, *predicate, *inserter);
   s = new Shape(Sphere( Vector(0.,0.,0.05), 0.1));
 
@@ -100 +102 @@
   delete mesh;
   delete predicate;
+  delete inserter;
 
   World::purgeInstance();

src/Filling/unittests/FillerUnitTest.hpp

@@ -25 +25 @@
 class Filler;
 class FillPredicate;
+class Inserter;
 class Mesh;
 class Shape;
@@ -46 +47 @@
       FillPredicate *predicate;
       Mesh *mesh;
+      Inserter *inserter;
       Filler *filler;
       atom * _atom;