Changeset e2396e

Timestamp:

Oct 19, 2014, 5:13:11 PM (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:

8544b32

Parents:

aac19f

git-author:

Frederik Heber <heber@…> (10/04/14 08:44:54)

git-committer:

Frederik Heber <heber@…> (10/19/14 17:13:11)

Message:

Added check whether all points remain inside surface and whether it is convex to ConvexEnvelopeAction.

Location:

src

Files:

• Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) (2 diffs)
• Tesselation/tesselation.cpp (modified) (1 diff)
• Tesselation/tesselation.hpp (modified) (1 diff)

src/Actions/TesselationAction/ConvexEnvelopeAction.cpp ¶

@@ -75 +75 @@
     //RemoveAllBoundaryPoints(TesselStruct, mol, argv[argptr]);
     const double volumedifference = ConvexizeNonconvexEnvelope(TesselStruct, mol, params.filenameConvex.get().string().c_str());
+    // check whether tesselated structure is truly convex
+    if (!TesselStruct->isConvex()) {
+      ELOG(1, "Tesselated surface has not been properly convexized.");
+        Success = false;
+    } else {
+      LOG(2, "DEBUG: We do have a convex surface tesselation now.");
+    }
+    // we check whether all molecule's atoms are still inside
+    std::vector<std::string> outside_atoms;
+    for(molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter)
+      if (!TesselStruct->IsInnerPoint((*iter)->getPosition(), LCList))
+        outside_atoms.push_back((*iter)->getName());
+    if (outside_atoms.empty())
+      LOG(2, "DEBUG: All molecule's atoms are inside the tesselated, convex surface.");
+    else {
+      ELOG(1, "The following atoms are not inside the tesselated, convex surface:"
+          << outside_atoms);
+      Success = false;
+    }
+
     const double clustervolume = TesselStruct->getVolumeOfConvexEnvelope(configuration->GetIsAngstroem());
     LOG(0, "The tesselated volume area is " << clustervolume << " " << (configuration->GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3.");
@@ -84 +104 @@
     return Action::success;
   else {
-    STATUS("Failed to find the non convex border.");
+    STATUS(std::string("Failed to find the non convex border")
+        +std::string("containing all atoms")
+        +std::string("."));
     return Action::failure;
   }

src/Tesselation/tesselation.cpp ¶

@@ -1744 +1744 @@
 ;
 
+bool Tesselation::isConvex() const
+{
+  bool status = true;
+  // go through all lines on boundary
+  for (LineMap::const_iterator lineiter = LinesOnBoundary.begin();
+      lineiter != LinesOnBoundary.end(); ++lineiter) {
+    if (!lineiter->second->CheckConvexityCriterion()) {
+      LOG(2, "DEBUG: Line " << *lineiter->second << " is not convex.");
+      status = false;
+    }
+  }
+  return status;
+}
+
 /** Checks whether the quadragon of the two triangles connect to \a *Base is convex.
  * We look whether the closest point on \a *Base with respect to the other baseline is outside

src/Tesselation/tesselation.hpp ¶

@@ -88 +88 @@
     void RemoveTesselationPoint(class BoundaryPointSet *point);
     bool CheckDegeneracy(CandidateForTesselation &CandidateLine, const double RADIUS, const LinkedCell_deprecated *LC) const;
-
+    bool isConvex() const;
 
     // concave envelope