Changeset e65de8 for src/Actions/MapOfActions.cpp

Timestamp:

Jul 25, 2010, 9:43:56 PM (14 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:

a8a010

Parents:

521bbf

Message:

Fixed all correlations for new selected sets of molecules.

• MapOfActions: added missing action names point-correlation and surface-correlation.
• BUGFIX: AnalysisPairCorrelationAction::createDialog() - needs to query for multiple element_s_.
• BUGFIX: MapOfActions::queryCurrentValue() - added values twice, due to ..ID or Z was not set to -1 after push_back.
• TESTFIX: Analysis/* all needed --select-all-molecules in front.
• TESTFIX: Analysis/4 need additional --unselect-molecule-by-id 207 to avoid correlating againts itself.
• TESTFIX: changed all correlation unit tests, i.e. replaced TestList by allMolecules from getSelectedMolecules().
• analysis_correlation.[ch]pp:
  • Replaced MoleculeListClass by const std::vector<molecule *>
  • ActiveFlag check is removed, we hand over getSelectedMolecules() from World (or any other vector of molecules) instead.

File:

• src/Actions/MapOfActions.cpp (modified) (16 diffs)

src/Actions/MapOfActions.cpp

@@ -196 +196 @@
   DescriptionMap["output"] = "write output files";
   DescriptionMap["set-output"] = "specify output formats";
-  DescriptionMap["pair-correlation"] = "pair correlation analysis between two elements, element and point or element and surface";
+  DescriptionMap["pair-correlation"] = "pair correlation analysis between two elements";
   DescriptionMap["parse-xyz"] = "parse xyz file into World";
+  DescriptionMap["point-correlation"] = "pair correlation analysis between element and point";
   DescriptionMap["principal-axis-system"] = "calculate the principal axis system of the specified molecule";
   DescriptionMap["remove-atom"] = "remove a specified atom";
@@ -211 +212 @@
   DescriptionMap["set-output"] = "specify output formats";
   DescriptionMap["subgraph-dissect"] = "dissect the molecular system into molecules representing disconnected subgraphs";
+  DescriptionMap["surface-correlation"] = "pair correlation analysis between element and surface";
   DescriptionMap["suspend-in-water"] = "suspend the given molecule in water such that in the domain the mean density is as specified";
   DescriptionMap["translate-mol"] = "translate molecule by given vector";
@@ -234 +236 @@
   DescriptionMap["MaxDistance"] = "maximum distance in space";
   DescriptionMap["molecule-by-id"] = "index of a molecule";
-  DescriptionMap["molecule-by-name"] = "name of a molecule";
   DescriptionMap["nonconvex-file"] = "filename of the non-convex envelope";
   DescriptionMap["order"] = "order of a discretization, dissection, ...";
@@ -271 +272 @@
   ShortFormMap["nonconvex-envelope"] = "N";
 //  ShortFormMap["output"] = "o";
-  ShortFormMap["pair-correlation"] = "C";
+//  ShortFormMap["pair-correlation"] = "C";
   ShortFormMap["parse-xyz"] = "p";
   ShortFormMap["remove-atom"] = "r";
@@ -312 +313 @@
   TypeMap["output"] = &typeid(void);
   TypeMap["parse-xyz"] = &typeid(std::string);
-  TypeMap["pair-correlation"] = &typeid(std::string);
+  TypeMap["pair-correlation"] = &typeid(void);
+  TypeMap["point-correlation"] = &typeid(void);
   TypeMap["principal-axis-system"] = &typeid(molecule);
   TypeMap["remove-atom"] = &typeid(void);
@@ -325 +327 @@
   TypeMap["set-output"] = &typeid(std::vector<std::string>);
   TypeMap["subgraph-dissect"] = &typeid(void);
+  TypeMap["surface-correlation"] = &typeid(void);
   TypeMap["suspend-in-water"] = &typeid(double);
   TypeMap["translate-mol"] = &typeid(VectorValue);
@@ -346 +349 @@
   TypeMap["lengths"] = &typeid(VectorValue);
   TypeMap["MaxDistance"] = &typeid(double);
+  TypeMap["molecule-by-id"] = &typeid(molecule);
   TypeMap["nonconvex-file"] = &typeid(std::string);
   TypeMap["order"] = &typeid(int);
@@ -382 +386 @@
   CurrentValue["bin-width"] = "0.5";
   CurrentValue["fastparsing"] = "0";
-  CurrentValue["atom-by-id"] = "-1";
-  CurrentValue["molecule-by-id"] = "-1";
   CurrentValue["periodic"] = "0";
 
@@ -399 +401 @@
   MenuContainsActionMap.insert( pair<std::string, std::string> ("analysis", "molecular-volume") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("analysis", "pair-correlation") );
+  MenuContainsActionMap.insert( pair<std::string, std::string> ("analysis", "point-correlation") );
+  MenuContainsActionMap.insert( pair<std::string, std::string> ("analysis", "surface-correlation") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("analysis", "principal-axis-system") );
 
@@ -478 +482 @@
         generic.insert("pair-correlation");
         generic.insert("parse-xyz");
+  generic.insert("point-correlation");
 //  generic.insert("principal-axis-system");
   generic.insert("remove-atom");
@@ -494 +499 @@
   generic.insert("set-output");
         generic.insert("subgraph-dissect");
+  generic.insert("surface-correlation");
   generic.insert("suspend-in-water");
   generic.insert("translate-mol");
@@ -522 +528 @@
   hidden.insert("lengths");
   hidden.insert("MaxDistance");
+  hidden.insert("molecule-by-id");
   hidden.insert("nonconvex-file");
   hidden.insert("order");
@@ -624 +631 @@
     CurrentValue.erase(name);
     while (!stream.fail()) {
-      stream >> atomID;
+      stream >> atomID >> ws;
       Walker = World::getInstance().getAtom(AtomById(atomID));
       if (Walker != NULL)
         _T.push_back(Walker);
+      atomID = -1;
+      Walker = NULL;
     }
   } else
@@ -643 +652 @@
     CurrentValue.erase(name);
     while (!stream.fail()) {
-      stream >> Z;
+      stream >> Z >> ws;
       elemental = World::getInstance().getPeriode()->FindElement(Z);
       if (elemental != NULL)
         _T.push_back(elemental);
+      Z = -1;
     }
   } else
@@ -662 +672 @@
     CurrentValue.erase(name);
     while (!stream.fail()) {
-      stream >> molID;
+      stream >> molID >> ws;
       mol = World::getInstance().getMolecule(MoleculeById(molID));
       if (mol != NULL)
         _T.push_back(mol);
+      molID = -1;
+      mol = NULL;
     }
   } else
@@ -842 +854 @@
     for (set<string>::iterator OptionRunner = ListRunner->first->begin(); OptionRunner != ListRunner->first->end(); ++OptionRunner) {
       if (hasValue(*OptionRunner)) {
-        DoLog(0) && (Log() << Verbose(0) << "Adding option " << *OptionRunner << " with type " << TypeMap[*OptionRunner]->name() << " to CommandLineParser." << endl);
+        DoLog(1) && (Log() << Verbose(1) << "Adding option " << *OptionRunner << " with type " << TypeMap[*OptionRunner]->name() << " to CommandLineParser." << endl);
            switch(TypeEnumMap[TypeMap[*OptionRunner]]) {
           default: