Changeset 6866aa for src

Timestamp:

Jun 11, 2010, 3:59:53 PM (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, 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:

f6bd32

Parents:

a307af

Message:

Case 'I' is now handled by CommandLineUI.

Location:

src

Files:

• Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) (2 diffs)
• Actions/MapOfActions.cpp (modified) (4 diffs)
• builder.cpp (modified) (1 diff)

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

@@ -24 +24 @@
 #include "Actions/MapOfActions.hpp"
 
-const char FragmentationSubgraphDissectionAction::NAME[] = "subspace-dissect";
+const char FragmentationSubgraphDissectionAction::NAME[] = "subgraph-dissect";
 
 FragmentationSubgraphDissectionAction::FragmentationSubgraphDissectionAction() :
@@ -39 +39 @@
 
   if(dialog->display()) {
+    DoLog(1) && (Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl);
+    // @TODO rather do the dissection afterwards
+    MoleculeListClass *molecules = World::getInstance().getMolecules();
+    molecules->DissectMoleculeIntoConnectedSubgraphs(World::getInstance().getPeriode(), World::getInstance().getConfig());
     delete dialog;
     return Action::success;

src/Actions/MapOfActions.cpp

@@ -96 +96 @@
   DescriptionMap["save-temperature"] = "name of the temperature file to write to";
   DescriptionMap["scale-box"] = "scale box and atomic positions inside";
-  DescriptionMap["subspace-dissect"] = "dissect the molecular system into molecules representing disconnected subgraphs";
+  DescriptionMap["subgraph-dissect"] = "dissect the molecular system into molecules representing disconnected subgraphs";
   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";
@@ -158 +158 @@
   ShortFormMap["scale-box"] = "s";
   ShortFormMap["set-basis"] = "M";
-  ShortFormMap["subspace-dissect"] = "I";
+  ShortFormMap["subgraph-dissect"] = "I";
   ShortFormMap["suspend-in-water"] = "u";
   ShortFormMap["translate-mol"] = "t";
@@ -197 +197 @@
   TypeMap["scale-box"] = Vector;
   TypeMap["set-basis"] = String;
+  TypeMap["subgraph-dissect"] = None;
   TypeMap["suspend-in-water"] = Double;
   TypeMap["translate-mol"] = Vector;
@@ -268 +269 @@
   generic.insert("scale-box");
   generic.insert("set-basis");
-//      generic.insert("subspace-dissect");
+        generic.insert("subgraph-dissect");
   generic.insert("suspend-in-water");
   generic.insert("translate-mol");

src/builder.cpp

@@ -1737 +1737 @@
             case 'I':
               DoLog(1) && (Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl);
-              // @TODO rather do the dissection afterwards
-              molecules->DissectMoleculeIntoConnectedSubgraphs(periode, &configuration);
-              mol = NULL;
-              if (molecules->ListOfMolecules.size() != 0) {
-                for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
-                  if ((*ListRunner)->ActiveFlag) {
-                    mol = *ListRunner;
-                    break;
-                  }
-              }
-              if ((mol == NULL) && (!molecules->ListOfMolecules.empty())) {
-                mol = *(molecules->ListOfMolecules.begin());
-                if (mol != NULL)
-                  mol->ActiveFlag = true;
-              }
+              ArgcList.insert(argptr-1);
+              argptr+=0;
               break;
             case 'C':