Changeset d4fa23

Timestamp:

Aug 21, 2009, 12:17:52 PM (15 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:

065e82

Parents:

9ba9ee

Message:

New function RemoveAllBoundaryPoints() for sequentially removing all boundary points.

• This is meant as a pre-test for the ConvexizeNonconvexTesselation().
• new function is incorporated into builder.cpp:ParseCommandLineOptions for case 'o'

Location:

src

Files:

• boundary.cpp (modified) (1 diff)
• boundary.hpp (modified) (1 diff)
• builder.cpp (modified) (1 diff)

src/boundary.cpp

@@ -578 +578 @@
 };
 
+/** For testing removes one boundary point after another to check for leaks.
+ * \param *out output stream for debugging
+ * \param *TesselStruct Tesselation containing envelope with boundary points
+ * \param *mol molecule
+ * \param *filename name of file
+ * \return true - all removed, false - something went wrong
+ */
+bool RemoveAllBoundaryPoints(ofstream *out, class Tesselation *TesselStruct, molecule *mol, char *filename)
+{
+  int i=0;
+  char number[MAXSTRINGSIZE];
+
+  if ((TesselStruct == NULL) || (TesselStruct->PointsOnBoundary.empty())) {
+    *out << Verbose(2) << "ERROR: TesselStruct is empty." << endl;
+    return false;
+  }
+
+  PointMap::iterator PointRunner;
+  while (!TesselStruct->PointsOnBoundary.empty()) {
+    *out << Verbose(2) << "Remaining points are: ";
+    for (PointMap::iterator PointSprinter = TesselStruct->PointsOnBoundary.begin(); PointSprinter != TesselStruct->PointsOnBoundary.end(); PointSprinter++)
+      *out << *(PointSprinter->second) << "\t";
+      *out << endl;
+
+    PointRunner = TesselStruct->PointsOnBoundary.begin();
+    // remove point
+    TesselStruct->RemovePointFromTesselatedSurface(out, PointRunner->second);
+
+    // store envelope
+    sprintf(number, "-%04d", i++);
+    StoreTrianglesinFile(out, mol, filename, number);
+  }
+
+  return true;
+};
+
 /** Creates a convex envelope from a given non-convex one.
  * -# First step, remove concave spots, i.e. singular "dents"

src/boundary.hpp

@@ -44 +44 @@
 void CalculateConcavityPerBoundaryPoint(ofstream *out, class Tesselation *TesselStruct);
 void StoreTrianglesinFile(ofstream *out, molecule *mol, const char *filename, const char *extraSuffix);
+bool RemoveAllBoundaryPoints(ofstream *out, class Tesselation *TesselStruct, molecule *mol, char *filename);
 
 

src/builder.cpp

@@ -1873 +1873 @@
                 //FindConvexBorder((ofstream *)&cout, mol, &LCList, argv[argptr]);
                 FindNonConvexBorder((ofstream *)&cout, mol, &LCList, argv[argptr], 10.);
-
-                double volumedifference = ConvexizeNonconvexEnvelope((ofstream *)&cout, mol->TesselStruct, mol, argv[argptr]);
-                double clustervolume = VolumeOfConvexEnvelope((ofstream *)&cout, mol->TesselStruct, &configuration);
-                cout << Verbose(0) << "The tesselated volume area is " << clustervolume << " " << (configuration.GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3." << endl;
-                cout << Verbose(0) << "The non-convex tesselated volume area is " << clustervolume-volumedifference << " " << (configuration.GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3." << endl;
+                RemoveAllBoundaryPoints((ofstream *)&cout, mol->TesselStruct, mol, argv[argptr]);
+//                double volumedifference = ConvexizeNonconvexEnvelope((ofstream *)&cout, mol->TesselStruct, mol, argv[argptr]);
+//                double clustervolume = VolumeOfConvexEnvelope((ofstream *)&cout, mol->TesselStruct, &configuration);
+//                cout << Verbose(0) << "The tesselated volume area is " << clustervolume << " " << (configuration.GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3." << endl;
+//                cout << Verbose(0) << "The non-convex tesselated volume area is " << clustervolume-volumedifference << " " << (configuration.GetIsAngstroem() ? "angstrom" : "atomiclength") << "^3." << endl;
                 argptr+=1;
               }