Changeset df0c80 for src/Filling

Timestamp:

Feb 28, 2016, 6:00:02 PM (9 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:

af340c

Parents:

b9d387

git-author:

Frederik Heber <heber@…> (02/16/16 13:49:23)

git-committer:

Frederik Heber <heber@…> (02/28/16 18:00:02)

Message:

FIX: Filling actions did not use minimum distance for tesselated surface.

• added IsCloseEnoughSurface_FillPredicate which requires a minimum distance to the tesselated surface (but does not care about the sign) and combines it with an additonal IsInsideSurface_FillPredicate.
• this is now used in regular-grid, surface, and volume fill actions when a non-zero minimum distance is given.
• TESTFIX: Test is now working.

Location:

src/Filling

Files:

• Makefile.am (modified) (2 diffs)
• Predicates/IsCloseEnoughToSurface_FillPredicate.cpp (added)
• Predicates/IsCloseEnoughToSurface_FillPredicate.hpp (added)
• Predicates/IsInsideSurface_FillPredicate.cpp (modified) (1 diff)
• Preparators/BaseFillerPreparator.cpp (modified) (3 diffs)
• Preparators/BaseFillerPreparator.hpp (modified) (1 diff)

src/Filling/Makefile.am

@@ -16 +16 @@
         Filling/Predicates/AnyFillPredicate.cpp \
         Filling/Predicates/FillPredicate.cpp \
+        Filling/Predicates/IsCloseEnoughToSurface_FillPredicate.cpp \
         Filling/Predicates/IsInsideDomain_FillPredicate.cpp \
         Filling/Predicates/IsInsideSurface_FillPredicate.cpp \
@@ -45 +46 @@
         Filling/Predicates/FillPredicateBase.hpp \
         Filling/Predicates/FillPredicate_impl.hpp \
+        Filling/Predicates/IsCloseEnoughToSurface_FillPredicate.hpp \
         Filling/Predicates/IsInsideDomain_FillPredicate.hpp \
         Filling/Predicates/IsInsideSurface_FillPredicate.hpp \

src/Filling/Predicates/IsInsideSurface_FillPredicate.cpp

@@ -46 +46 @@
 FillPredicate IsInsideSurface_FillPredicate(const Tesselation &_tess, const LinkedCell_deprecated &_LC)
 {
-  AnyFillPredicate::FillPredicator function = boost::bind(&Tesselation::IsInnerPoint, &_tess, _1, &_LC);
+  AnyFillPredicate::FillPredicator function =
+                  boost::bind(&Tesselation::IsInnerPoint, boost::cref(_tess), _1, &_LC);
   FillPredicate::impl_ptr impl(new AnyFillPredicate(function));
   return FillPredicate(impl);

src/Filling/Preparators/BaseFillerPreparator.cpp

@@ -46 +46 @@
 #include "Filling/Mesh/CubeMesh.hpp"
 #include "Filling/Mesh/MeshAdaptor.hpp"
+#include "Filling/Predicates/IsCloseEnoughToSurface_FillPredicate.hpp"
 #include "Filling/Predicates/IsInsideSurface_FillPredicate.hpp"
 #include "Filling/Predicates/IsVoidNode_FillPredicate.hpp"
@@ -85 +86 @@
 void BaseFillerPreparator::addSurfacePredicate(
     const double _radius,
-    std::vector<atom *> &_atoms)
+    std::vector<atom *> &_atoms,
+    const double minimum_distance)
 {
   // create adaptor for the selected atoms
@@ -96 +98 @@
 
   // and create predicate
-  surface_predicate = new FillPredicate( IsInsideSurface_FillPredicate( *TesselStruct, *LC ) );
+  if (minimum_distance == 0.)
+          surface_predicate =
+                          new FillPredicate( IsInsideSurface_FillPredicate(
+                                          *TesselStruct, *LC ) );
+  else
+          surface_predicate =
+                          new FillPredicate( IsCloseEnoughToSurface_FillPredicate(
+                                          *TesselStruct, *LC, minimum_distance ) );
 }
 

src/Filling/Preparators/BaseFillerPreparator.hpp

@@ -40 +40 @@
   void addSurfacePredicate(
       const double _radius,
-      std::vector<atom *> &_atoms);
+      std::vector<atom *> &_atoms,
+      const double minimum_distance = 0.);
   void addRandomInserter(
       const double _RandAtomDisplacement,