Changeset bcb831

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:

5f7b95

Parents:

991c35

git-author:

Frederik Heber <heber@…> (09/25/14 16:24:30)

git-committer:

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

Message:

Added SphereRadius parameter to ConvexEnvelopeAction.

Files:

• src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) (1 diff)
• src/Actions/TesselationAction/ConvexEnvelopeAction.def (modified) (2 diffs)
• tests/Python/AllActions/options.dat (modified) (1 diff)
• tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) (1 diff)

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());

src/Actions/TesselationAction/ConvexEnvelopeAction.def

@@ -10 +10 @@
 
 #include "Parameters/Validators/Ops_Validator.hpp"
+#include "Parameters/Validators/Specific/BoxLengthValidator.hpp"
 #include "Parameters/Validators/Specific/FilePresentValidator.hpp"
 
@@ -15 +16 @@
 // 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")
+#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 (filenameConvex)(filenameNonConvex)
+#define paramreferences (SphereRadius)(filenameConvex)(filenameNonConvex)
 #define paramvalids \
+(BoxLengthValidator()) \
 (!FilePresentValidator()) \
 (!FilePresentValidator())

tests/Python/AllActions/options.dat

@@ -42 +42 @@
 change-element  "1"
 change-molname  "water"
+convex-envelope "50."
 convex-file     "convexfile"
 copy-molecule   "0"

tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at

@@ -24 +24 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Tesselation/Convex/pre/test.conf $file], 0)
 convexfile=ConvexEnvelope
-AT_CHECK([../../molecuilder -i $file  --select-molecule-by-id 0 --convex-envelope --convex-file $convexfile --nonconvex-file NonConvexEnvelope], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $file  --select-molecule-by-id 0 --convex-envelope 50. --convex-file $convexfile --nonconvex-file NonConvexEnvelope], 0, [stdout], [stderr])
 AT_CHECK([diff ${convexfile}.dat ${abs_top_srcdir}/tests/regression/Tesselation/Convex/post/ConvexEnvelope.dat], 0, [ignore], [ignore])
 #AT_CHECK([diff ${convexfile}.r3d ${abs_top_srcdir}/tests/regression/Tesselation/Convex/post/ConvexEnvelope.r3d], 0, [ignore], [ignore])