Changeset 0516fd for src/Actions/TesselationAction

Timestamp:

Oct 19, 2014, 5:13:32 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:

e63edb

Parents:

3b1798 (diff), 33ee99 (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 'Fix_ConvexizeNonconvexEnvelope' into Candidate_v1.4.9

Location:

src/Actions/TesselationAction

Files:

• ConvexEnvelopeAction.cpp (modified) (2 diffs)
• ConvexEnvelopeAction.def (modified) (2 diffs)

src/Actions/TesselationAction/ConvexEnvelopeAction.cpp

@@ -68 +68 @@
     LOG(1, "Storing tecplot non-convex data in " << params.filenameNonConvex.get() << ".");
     PointCloudAdaptor<molecule> cloud(mol, mol->name);
-    LCList = new LinkedCell_deprecated(cloud, 100.);
+    LCList = new LinkedCell_deprecated(cloud, 2.*params.SphereRadius.get());
     //Boundaries *BoundaryPoints = NULL;
     //FindConvexBorder(mol, BoundaryPoints, TesselStruct, LCList, argv[argptr]);
     // TODO: Beide Funktionen sollten streams anstelle des Filenamen benutzen, besser fuer unit tests
-    Success &= FindNonConvexBorder(mol, TesselStruct, LCList, 50., params.filenameNonConvex.get().string().c_str());
+    Success &= FindNonConvexBorder(mol, TesselStruct, LCList, params.SphereRadius.get(), params.filenameNonConvex.get().string().c_str());
     //RemoveAllBoundaryPoints(TesselStruct, mol, argv[argptr]);
-    const double volumedifference = ConvexizeNonconvexEnvelope(TesselStruct, mol, params.filenameConvex.get().string().c_str());
+    const double volumedifference =
+        ConvexizeNonconvexEnvelope(TesselStruct, mol, params.filenameConvex.get().string().c_str(),
+            params.DoOutputEveryStep.get());
+    // 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 +106 @@
     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/Actions/TesselationAction/ConvexEnvelopeAction.def

@@ -9 +9 @@
 class TesselationListClass;
 
+#include "Parameters/Validators/DummyValidator.hpp"
 #include "Parameters/Validators/Ops_Validator.hpp"
+#include "Parameters/Validators/Specific/BoxLengthValidator.hpp"
 #include "Parameters/Validators/Specific/FilePresentValidator.hpp"
 
@@ -15 +17 @@
 // 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 (boost::filesystem::path)(boost::filesystem::path)
-#define paramtokens ("convex-file")("nonconvex-file")
-#define paramdescriptions ("filename of the convex envelope")("filename of the non-convex envelope")
-#undef paramdefaults
-#define paramreferences (filenameConvex)(filenameNonConvex)
+#define paramtypes (double)(boost::filesystem::path)(boost::filesystem::path)(bool)
+#define paramtokens ("convex-envelope")("convex-file")("nonconvex-file")("DoOutputEveryStep")
+#define paramdescriptions ("radius of the rolling sphere")("filename of the convex envelope")("filename of the non-convex envelope")("whether to write an extra file for debugging of each convexization step")
+#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(0))
+#define paramreferences (SphereRadius)(filenameConvex)(filenameNonConvex)(DoOutputEveryStep)
 #define paramvalids \
+(BoxLengthValidator()) \
 (!FilePresentValidator()) \
-(!FilePresentValidator())
+(!FilePresentValidator()) \
+(DummyValidator<bool>())
 
 #undef statetypes