Changeset 7951b9 for src/Actions/AnalysisAction

Timestamp:

Jun 13, 2012, 5:39:01 PM (13 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:

2382d7

Parents:

e45c1d

git-author:

Frederik Heber <heber@…> (05/10/12 08:38:35)

git-committer:

Frederik Heber <heber@…> (06/13/12 17:39:01)

Message:

Rewrote SurfaceCorrelationAction such that selected atoms are used in replacement of parameter surfacemol.

• We must not request atoms or molecules inside action parameters. These must be obtained via prior selections.

Location:

src/Actions/AnalysisAction

Files:

• SurfaceCorrelationAction.cpp (modified) (2 diffs)
• SurfaceCorrelationAction.def (modified) (1 diff)

src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

@@ -55 +55 @@
   output.open(params.outputname.get().string().c_str());
   binoutput.open(params.binoutputname.get().string().c_str());
-  molecule *surfacemol = const_cast<molecule *>(params.Boundary.get());
-  ASSERT(surfacemol != NULL, "No molecule specified for SurfaceCorrelation.");
+
+  // check for selected molecules and create surfaces from them
+  std::vector<atom *> atoms(World::getInstance().getSelectedAtoms());
+  LinkedCell_deprecated * LCList = NULL;
+  Tesselation * TesselStruct = NULL;
   const double radius = 4.;
   double LCWidth = 20.;
@@ -65 +68 @@
       LCWidth = 2.*radius;
   }
+  if ( atoms.size() == 0) {
+    ELOG(1, "You have not select any atoms.");
+    return Action::failure;
+  }
+  // create adaptor for the selected atoms
+  PointCloudAdaptor< std::vector<atom *> > cloud(&atoms, std::string("Selected atoms"));
 
-  // get the boundary
-  class Tesselation *TesselStruct = NULL;
-  const LinkedCell_deprecated *LCList = NULL;
-  // find biggest molecule
+  // create tesselation
+  LCList = new LinkedCell_deprecated(cloud, 2.*radius);
+  TesselStruct = new Tesselation;
+  (*TesselStruct)(cloud, radius);
+
+  // correlate
   std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
   std::cout << "There are " << molecules.size() << " selected molecules." << std::endl;
-  PointCloudAdaptor<molecule> cloud(surfacemol, surfacemol->name);
-  LCList = new LinkedCell_deprecated(cloud, LCWidth);
-  FindNonConvexBorder(surfacemol, TesselStruct, LCList, radius, NULL);
   CorrelationToSurfaceMap *surfacemap = NULL;
   if (params.periodic.get())

src/Actions/AnalysisAction/SurfaceCorrelationAction.def

@@ -15 +15 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
-#define paramtypes (std::vector<const element *>)(const molecule *)(double)(double)(double)(boost::filesystem::path)(boost::filesystem::path)(bool)
-#define paramreferences (elements)(Boundary)(BinStart)(BinWidth)(BinEnd)(outputname)(binoutputname)(periodic)
-#define paramtokens ("elements")("molecule-by-id")("bin-start")("bin-width")("bin-end")("output-file")("bin-output-file")("periodic")
-#define paramdescriptions ("set of elements")("index of a molecule")("start of the first bin")("width of the bins")("start of the last bin")("name of the output file")("name of the bin output file")("system is constraint to periodic boundary conditions")
-#define paramdefaults (NODEFAULT)(NODEFAULT)(NODEFAULT)("0.5")(NODEFAULT)(NODEFAULT)(NODEFAULT)("0")
+#define paramtypes (std::vector<const element *>)(double)(double)(double)(boost::filesystem::path)(boost::filesystem::path)(bool)
+#define paramreferences (elements)(BinStart)(BinWidth)(BinEnd)(outputname)(binoutputname)(periodic)
+#define paramtokens ("elements")("bin-start")("bin-width")("bin-end")("output-file")("bin-output-file")("periodic")
+#define paramdescriptions ("set of elements")("start of the first bin")("width of the bins")("start of the last bin")("name of the output file")("name of the bin output file")("system is constraint to periodic boundary conditions")
+#define paramdefaults (NODEFAULT)(NODEFAULT)("0.5")(NODEFAULT)(NODEFAULT)(NODEFAULT)("0")
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS