Changeset 9ee38b for src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

Timestamp:

Aug 28, 2010, 12:52:58 AM (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, Candidate_v1.7.0, 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:

b4fa106

Parents:

0b2ce9

git-author:

Frederik Heber <heber@…> (08/25/10 17:20:37)

git-committer:

Frederik Heber <heber@…> (08/28/10 00:52:58)

Message:

Extended macro framework.

Extensions:

• all central definitions reside in .def files
  • This if file is necessary because we need the definitions at two places: hpp and cpp
  • And as we always use the same define names, we have to undefine them at the end of both (otherwise we get compiler warnings and are prone to dumb mistakes of forgotten defines seeming present)
• the .hpp is just a very tiny header, that should be possible to batch- construct inside Makefile as well
• .cpp includes some Action_...hpp files and implements the function

For later (i.e. when ActionRegistry becomes prototype copier)

• instead of waiting for clone(), for now we simply call the prototype.
• in the action command we must not yet prefix paramreferences with "params."

Changes:

• Dialog::query<> is a template which is specialized for every present query...() function. We need it to automatize fillDialog()
• all AnalysisAction's are now converted, i.e. framework is functional with parameters and queries (MolecularVolume had none).

File:

• src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) (5 diffs)

src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

@@ -20 +20 @@
 #include "Helpers/MemDebug.hpp"
 
-#include "Actions/AnalysisAction/SurfaceCorrelationAction.hpp"
-#include "Actions/ActionRegistry.hpp"
 #include "analysis_correlation.hpp"
 #include "boundary.hpp"
@@ -39 +37 @@
 using namespace std;
 
-#include "UIElements/UIFactory.hpp"
-#include "UIElements/Dialog.hpp"
-#include "Actions/ValueStorage.hpp"
+#include "Actions/AnalysisAction/SurfaceCorrelationAction.hpp"
 
-const char AnalysisSurfaceCorrelationAction::NAME[] = "surface-correlation";
+// and construct the stuff
+#include "SurfaceCorrelationAction.def"
+#include "Action_impl_pre.hpp"
 
-AnalysisSurfaceCorrelationAction::AnalysisSurfaceCorrelationAction() :
-  Action(NAME)
-{}
-
-AnalysisSurfaceCorrelationAction::~AnalysisSurfaceCorrelationAction()
-{}
-
-void AnalysisSurfaceCorrelation(std::vector< element *> &elements, molecule *mol, double BinStart, double BinWidth, double BinEnd, std::string &outputname, std::string &binoutputname, bool periodic) {
-  ValueStorage::getInstance().setCurrentValue("elements", elements);
-  ValueStorage::getInstance().setCurrentValue("molecule-by-id", mol);
-  ValueStorage::getInstance().setCurrentValue("bin-start", BinStart);
-  ValueStorage::getInstance().setCurrentValue("bin-width", BinWidth);
-  ValueStorage::getInstance().setCurrentValue("bin-end", BinEnd);
-  ValueStorage::getInstance().setCurrentValue("output-file", outputname);
-  ValueStorage::getInstance().setCurrentValue("bin-output-file", binoutputname);
-  ValueStorage::getInstance().setCurrentValue("periodic", periodic);
-  ActionRegistry::getInstance().getActionByName(AnalysisSurfaceCorrelationAction::NAME)->call(Action::NonInteractive);
-};
-
-
-void AnalysisSurfaceCorrelationAction::getParametersfromValueStorage()
-{};
-
-Dialog* AnalysisSurfaceCorrelationAction::fillDialog(Dialog *dialog) {
-  ASSERT(dialog,"No Dialog given when filling action dialog");
-
-  dialog->queryMolecule("molecule-by-id", ValueStorage::getInstance().getDescription("molecule-by-id"));
-  dialog->queryElements("elements", ValueStorage::getInstance().getDescription("elements"));
-  dialog->queryDouble("bin-start", ValueStorage::getInstance().getDescription("bin-start"));
-  dialog->queryDouble("bin-width", ValueStorage::getInstance().getDescription("bin-width"));
-  dialog->queryDouble("bin-end", ValueStorage::getInstance().getDescription("bin-end"));
-  dialog->queryString("output-file", ValueStorage::getInstance().getDescription("output-file"));
-  dialog->queryString("bin-output-file", ValueStorage::getInstance().getDescription("bin-output-file"));
-  dialog->queryBoolean("periodic", ValueStorage::getInstance().getDescription("periodic"));
-
-  return dialog;
-}
-
+/** =========== define the function ====================== */
 Action::state_ptr AnalysisSurfaceCorrelationAction::performCall() {
   int ranges[3] = {1, 1, 1};
-  double BinEnd = 0.;
-  double BinStart = 0.;
-  double BinWidth = 0.;
-  molecule *Boundary = NULL;
-  string outputname;
-  string binoutputname;
-  bool periodic;
   ofstream output;
   ofstream binoutput;
-  std::vector<const element *> elements;
   string type;
-  Vector Point;
   BinPairMap *binmap = NULL;
 
   // obtain information
-  ValueStorage::getInstance().queryCurrentValue("molecule-by-id", Boundary);
-  ValueStorage::getInstance().queryCurrentValue("elements", elements);
-  ValueStorage::getInstance().queryCurrentValue("bin-start", BinStart);
-  ValueStorage::getInstance().queryCurrentValue("bin-width", BinWidth);
-  ValueStorage::getInstance().queryCurrentValue("bin-end", BinEnd);
-  ValueStorage::getInstance().queryCurrentValue("output-file", outputname);
-  ValueStorage::getInstance().queryCurrentValue("bin-output-file", binoutputname);
-  ValueStorage::getInstance().queryCurrentValue("periodic", periodic);
+  getParametersfromValueStorage();
 
   // execute action
-  output.open(outputname.c_str());
-  binoutput.open(binoutputname.c_str());
-  ASSERT(Boundary != NULL, "No molecule specified for SurfaceCorrelation.");
+  output.open(params.outputname.c_str());
+  binoutput.open(params.binoutputname.c_str());
+  ASSERT(params.Boundary != NULL, "No molecule specified for SurfaceCorrelation.");
   const double radius = 4.;
   double LCWidth = 20.;
-  if (BinEnd > 0) {
-    if (BinEnd > 2.*radius)
-      LCWidth = BinEnd;
+  if (params.BinEnd > 0) {
+    if (params.BinEnd > 2.*radius)
+      LCWidth = params.BinEnd;
     else
       LCWidth = 2.*radius;
@@ -128 +73 @@
   std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
   std::cout << "There are " << molecules.size() << " selected molecules." << std::endl;
-  LCList = new LinkedCell(Boundary, LCWidth);
-  FindNonConvexBorder(Boundary, TesselStruct, LCList, radius, NULL);
+  LCList = new LinkedCell(params.Boundary, LCWidth);
+  FindNonConvexBorder(params.Boundary, TesselStruct, LCList, radius, NULL);
   CorrelationToSurfaceMap *surfacemap = NULL;
-  if (periodic)
-    surfacemap = PeriodicCorrelationToSurface( molecules, elements, TesselStruct, LCList, ranges);
+  if (params.periodic)
+    surfacemap = PeriodicCorrelationToSurface( molecules, params.elements, TesselStruct, LCList, ranges);
   else
-    surfacemap = CorrelationToSurface( molecules, elements, TesselStruct, LCList);
+    surfacemap = CorrelationToSurface( molecules, params.elements, TesselStruct, LCList);
   delete LCList;
   OutputCorrelationToSurface(&output, surfacemap);
@@ -144 +89 @@
       DoeLog(1) && (eLog()<< Verbose(1) << "Linked Cell width is smaller than the found range of values! Bins can only be correct up to: " << radius << "." << endl);
   }
-  binmap = BinData( surfacemap, BinWidth, BinStart, BinEnd );
+  binmap = BinData( surfacemap, params.BinWidth, params.BinStart, params.BinEnd );
   OutputCorrelation ( &binoutput, binmap );
   delete TesselStruct;  // surfacemap contains refs to triangles! delete here, not earlier!
@@ -173 +118 @@
   return NAME;
 }
+/** =========== end of function ====================== */