Changeset b7fbf0

Timestamp:

Apr 18, 2011, 3:43:58 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:

3bd460a

Parents:

b404da

git-author:

Frederik Heber <heber@…> (04/18/11 15:42:35)

git-committer:

Frederik Heber <heber@…> (04/18/11 15:43:58)

Message:

FIX: select-molecule-by-id crashed when no molecules are present.

• each molecule selection action checks whether molecules are present at all
• rewrote MoleculeByIdActions to take integer from command-line not molecule reference and perform the MoleculeById selection themselves (as do all other Actions, too).
• this fixes ticket #134.

Location:

src/Actions/SelectionAction/Molecules

Files:

• AllMoleculesAction.cpp (modified) (1 diff)
• ClearAllMoleculesAction.cpp (modified) (1 diff)
• MoleculeByFormulaAction.cpp (modified) (1 diff)
• MoleculeByIdAction.cpp (modified) (4 diffs)
• MoleculeByIdAction.def (modified) (1 diff)
• MoleculeByNameAction.cpp (modified) (1 diff)
• MoleculeByOrderAction.cpp (modified) (1 diff)
• MoleculeOfAtomAction.cpp (modified) (1 diff)
• NotAllMoleculesAction.cpp (modified) (1 diff)
• NotMoleculeByFormulaAction.cpp (modified) (1 diff)
• NotMoleculeByIdAction.cpp (modified) (4 diffs)
• NotMoleculeByIdAction.def (modified) (1 diff)
• NotMoleculeByNameAction.cpp (modified) (1 diff)
• NotMoleculeByOrderAction.cpp (modified) (1 diff)
• NotMoleculeOfAtomAction.cpp (modified) (1 diff)

src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp

@@ -43 +43 @@
   getParametersfromValueStorage();
 
+  // check whether molecules are present at all
+  if (World::getInstance().numMolecules() == 0) {
+    ELOG(1, "No molecules present in the world to select!");
+    return Action::failure;
+  }
+
   std::vector<molecule *> selectedMolecules = World::getInstance().getSelectedMolecules();
   DoLog(1) && (Log() << Verbose(1) << "Selecting all molecules." << endl);

src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp

@@ -42 +42 @@
   getParametersfromValueStorage();
 
+  // check whether molecules are present at all
+  if (World::getInstance().numMolecules() == 0) {
+    ELOG(1, "No molecules present in the world to select!");
+    return Action::failure;
+  }
+
   std::vector<molecule *> selectedMolecules = World::getInstance().getSelectedMolecules();
   DoLog(1) && (Log() << Verbose(1) << "Clearing molecule selection." << endl);

src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp

@@ -43 +43 @@
   getParametersfromValueStorage();
 
+  // check whether molecules are present at all
+  if (World::getInstance().numMolecules() == 0) {
+    ELOG(1, "No molecules present in the world to select!");
+    return Action::failure;
+  }
+
   DoLog(1) && (Log() << Verbose(1) << "Selecting molecules with chemical formula " << params.formula << ":" << endl);
 //  std::vector<molecule *> matchingMolecules = World::getInstance().getAllMolecules(MoleculeByFormula(params.formula));

src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp

@@ -23 +23 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "Descriptors/MoleculeIdDescriptor.hpp"
 #include "World.hpp"
 
@@ -40 +41 @@
   getParametersfromValueStorage();
 
-  if (params.mol != NULL) {
-    if (!World::getInstance().isSelected(params.mol)) {
-      DoLog(1) && (Log() << Verbose(1) << "Selecting molecule " << params.mol->name << endl);
-      World::getInstance().selectMolecule(params.mol);
+  // check whether molecules are present at all
+  if (World::getInstance().numMolecules() == 0) {
+    ELOG(1, "No molecules present in the world to select!");
+    return Action::failure;
+  }
+
+  const molecule *mol = World::getInstance().getMolecule(MoleculeById(params.molindex));
+  if (mol != NULL) {
+    if (!World::getInstance().isSelected(mol)) {
+      DoLog(1) && (Log() << Verbose(1) << "Selecting molecule " << mol->name << endl);
+      World::getInstance().selectAllMolecules(MoleculeById(params.molindex));
       DoLog(0) && (Log() << Verbose(0) << World::getInstance().countSelectedMolecules() << " molecules selected." << endl);
       return Action::state_ptr(new SelectionMoleculeByIdState(params));
@@ -57 +65 @@
   SelectionMoleculeByIdState *state = assert_cast<SelectionMoleculeByIdState*>(_state.get());
 
-  World::getInstance().unselectMolecule(state->params.mol);
+  World::getInstance().unselectAllMolecules(MoleculeById(state->params.molindex));
 
   return Action::state_ptr(_state);
@@ -65 +73 @@
   SelectionMoleculeByIdState *state = assert_cast<SelectionMoleculeByIdState*>(_state.get());
 
-  World::getInstance().selectMolecule(state->params.mol);
+  World::getInstance().selectAllMolecules(MoleculeById(state->params.molindex));
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Molecules/MoleculeByIdAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
-class molecule;
 
 // i.e. there is an integer with variable name Z that can be found in
 // 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 (const molecule*)
+#define paramtypes (int)
 #define paramtokens ("select-molecule-by-id")
 #define paramdescriptions ("molecule index")
 #undef paramdefaults
-#define paramreferences (mol)
+#define paramreferences (molindex)
 
 #undef statetypes

src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp

@@ -43 +43 @@
   getParametersfromValueStorage();
 
+  // check whether molecules are present at all
+  if (World::getInstance().numMolecules() == 0) {
+    ELOG(1, "No molecules present in the world to select!");
+    return Action::failure;
+  }
+
   DoLog(1) && (Log() << Verbose(1) << "Selecting all molecules called " << params.molname << endl);
   std::vector<molecule *> selectedMolecules =

src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp

@@ -42 +42 @@
   getParametersfromValueStorage();
 
+  // check whether molecules are present at all
+  if (World::getInstance().numMolecules() == 0) {
+    ELOG(1, "No molecules present in the world to select!");
+    return Action::failure;
+  }
+
   molecule *mol = World::getInstance().getMolecule(MoleculeByOrder(params.molindex));
 

src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp

@@ -42 +42 @@
   getParametersfromValueStorage();
 
+  // check whether molecules are present at all
+  if (World::getInstance().numMolecules() == 0) {
+    ELOG(1, "No molecules present in the world to select!");
+    return Action::failure;
+  }
+
   std::vector<molecule *> selectedMolecules = World::getInstance().getSelectedMolecules();
   DoLog(1) && (Log() << Verbose(1) << "Selecting molecule to currently selected atoms." << endl);

src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp

@@ -42 +42 @@
   getParametersfromValueStorage();
 
+  // check whether molecules are present at all
+  if (World::getInstance().numMolecules() == 0) {
+    ELOG(1, "No molecules present in the world to select!");
+    return Action::failure;
+  }
+
   std::vector<molecule *> selectedMolecules = World::getInstance().getSelectedMolecules();
   DoLog(1) && (Log() << Verbose(1) << "Unselecting all molecules." << endl);

src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp

@@ -43 +43 @@
   getParametersfromValueStorage();
 
+  // check whether molecules are present at all
+  if (World::getInstance().numMolecules() == 0) {
+    ELOG(1, "No molecules present in the world to select!");
+    return Action::failure;
+  }
+
   DoLog(1) && (Log() << Verbose(1) << "Unselecting molecules with chemical formula " << params.formula << ":" << endl);
   std::vector<molecule *> matchingMolecules = World::getInstance().getAllMolecules(MoleculeByFormula(params.formula));

src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp

@@ -23 +23 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "Descriptors/MoleculeIdDescriptor.hpp"
 #include "World.hpp"
 
@@ -40 +41 @@
   getParametersfromValueStorage();
 
-  if (params.mol != NULL) {
-    if (World::getInstance().isSelected(params.mol)) {
-      DoLog(1) && (Log() << Verbose(1) << "Unselecting molecule " << params.mol->name << endl);
-      World::getInstance().unselectMolecule(params.mol);
+  // check whether molecules are present at all
+  if (World::getInstance().numMolecules() == 0) {
+    ELOG(1, "No molecules present in the world to select!");
+    return Action::failure;
+  }
+
+  const molecule *mol = World::getInstance().getMolecule(MoleculeById(params.molindex));
+  if (mol != NULL) {
+    if (World::getInstance().isSelected(mol)) {
+      DoLog(1) && (Log() << Verbose(1) << "Unselecting molecule " << mol->name << endl);
+      World::getInstance().unselectAllMolecules(MoleculeById(params.molindex));
       DoLog(0) && (Log() << Verbose(0) << World::getInstance().countSelectedMolecules() << " molecules remain selected." << endl);
       return Action::state_ptr(new SelectionNotMoleculeByIdState(params));
@@ -57 +65 @@
   SelectionNotMoleculeByIdState *state = assert_cast<SelectionNotMoleculeByIdState*>(_state.get());
 
-  World::getInstance().selectMolecule(state->params.mol);
+  World::getInstance().selectAllMolecules(MoleculeById(state->params.molindex));
 
   return Action::state_ptr(_state);
@@ -65 +73 @@
   SelectionNotMoleculeByIdState *state = assert_cast<SelectionNotMoleculeByIdState*>(_state.get());
 
-  World::getInstance().unselectMolecule(state->params.mol);
+  World::getInstance().unselectAllMolecules(MoleculeById(state->params.molindex));
 
   return Action::state_ptr(_state);

src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.def

@@ -12 +12 @@
 // 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 (const molecule*)
+#define paramtypes (int)
 #define paramtokens ("unselect-molecule-by-id")
 #define paramdescriptions ("molecule index")
 #undef paramdefaults
-#define paramreferences (mol)
+#define paramreferences (molindex)
 
 #undef statetypes

src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp

@@ -43 +43 @@
   getParametersfromValueStorage();
 
+  // check whether molecules are present at all
+  if (World::getInstance().numMolecules() == 0) {
+    ELOG(1, "No molecules present in the world to select!");
+    return Action::failure;
+  }
+
   DoLog(1) && (Log() << Verbose(1) << "Unselecting all molecule called " << params.molname << endl);
   std::vector<molecule *> unselectedMolecules =

src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp

@@ -42 +42 @@
   getParametersfromValueStorage();
 
+  // check whether molecules are present at all
+  if (World::getInstance().numMolecules() == 0) {
+    ELOG(1, "No molecules present in the world to select!");
+    return Action::failure;
+  }
+
   molecule *mol = World::getInstance().getMolecule(MoleculeByOrder(params.molindex));
 

src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp

@@ -42 +42 @@
   getParametersfromValueStorage();
 
+  // check whether molecules are present at all
+  if (World::getInstance().numMolecules() == 0) {
+    ELOG(1, "No molecules present in the world to select!");
+    return Action::failure;
+  }
+
   std::vector<molecule *> unselectedMolecules = World::getInstance().getSelectedMolecules();
   DoLog(1) && (Log() << Verbose(1) << "Unselecting molecule to currently selected atoms." << endl);