Changeset 5f7b95

Timestamp:

Oct 19, 2014, 5:13:12 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:

565695

Parents:

bcb831

git-author:

Frederik Heber <heber@…> (10/09/14 09:47:03)

git-committer:

Frederik Heber <heber@…> (10/19/14 17:13:12)

Message:

Convex-envelope has debug parameter DoOutputEveryStep.

• this writes for each convexization step a distinct tesselation file.
• added parameter to ConvexizeNonconvexEnvelope().

Files:

• src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) (1 diff)
• src/Actions/TesselationAction/ConvexEnvelopeAction.def (modified) (2 diffs)
• src/Tesselation/boundary.cpp (modified) (3 diffs)
• src/Tesselation/boundary.hpp (modified) (1 diff)
• tests/Python/AllActions/options.dat (modified) (1 diff)

src/Actions/TesselationAction/ConvexEnvelopeAction.cpp

@@ -74 +74 @@
     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()) {

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"
@@ -16 +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 (double)(boost::filesystem::path)(boost::filesystem::path)
-#define paramtokens ("convex-envelope")("convex-file")("nonconvex-file")
-#define paramdescriptions ("radius of the rolling sphere")("filename of the convex envelope")("filename of the non-convex envelope")
-#undef paramdefaults
-#define paramreferences (SphereRadius)(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

src/Tesselation/boundary.cpp

@@ -513 +513 @@
  * \return volume difference between the non- and the created convex envelope
  */
-double ConvexizeNonconvexEnvelope(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename)
+double ConvexizeNonconvexEnvelope(
+    Tesselation *&TesselStruct,
+    const molecule * const mol,
+    const char * const filename,
+    bool DebugOutputEveryStep)
 {
         //Info FunctionInfo(__func__);
@@ -544 +548 @@
     Concavity = false;
 
-    sprintf(dummy, "-%d", run++);
-    //CalculateConcavityPerBoundaryPoint(TesselStruct);
-    LOG(1, "INFO: Writing " << run << "th tesselation file.");
-    StoreTrianglesinFile(mol, (const Tesselation *&)TesselStruct, filename, dummy);
+    if (DebugOutputEveryStep) {
+      sprintf(dummy, "-%d", run++);
+      //CalculateConcavityPerBoundaryPoint(TesselStruct);
+      LOG(1, "INFO: Writing " << run << "th tesselation file.");
+      StoreTrianglesinFile(mol, (const Tesselation *&)TesselStruct, filename, dummy);
+    }
 
     // first step: remove all full-concave point
@@ -575 +581 @@
     }
 
-    sprintf(dummy, "-%d", run++);
-    //CalculateConcavityPerBoundaryPoint(TesselStruct);
-    LOG(1, "INFO: Writing " << run << "th tesselation file.");
-    StoreTrianglesinFile(mol, (const Tesselation *&)TesselStruct, filename, dummy);
+    if (DebugOutputEveryStep) {
+      sprintf(dummy, "-%d", run++);
+      //CalculateConcavityPerBoundaryPoint(TesselStruct);
+      LOG(1, "INFO: Writing " << run << "th tesselation file.");
+      StoreTrianglesinFile(mol, (const Tesselation *&)TesselStruct, filename, dummy);
+    }
 
     // second step: flip baselines, i.e. add general tetraeder at concave lines

src/Tesselation/boundary.hpp

@@ -39 +39 @@
 /********************************************** declarations *******************************/
 
-double ConvexizeNonconvexEnvelope(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename);
+double ConvexizeNonconvexEnvelope(class Tesselation *&TesselStruct, const molecule * const mol, const char * const filename, bool DebugOutputEveryStep = false);
 void FindConvexBorder(const molecule* const mol, Boundaries *BoundaryPts, Tesselation *&TesselStruct, const LinkedCell_deprecated *LCList, const char *filename);
 Vector* FindEmbeddingHole(MoleculeListClass *mols, molecule *srcmol);

tests/Python/AllActions/options.dat

@@ -63 +63 @@
 DoCyclesFull    "0"
 DoLongrange     "0"
+DoOutputEveryStep       "0"
 DoPrintDebug    "0"
 DoRotate        "0"