Changeset b5c53d for src/Actions

Timestamp:

Aug 9, 2010, 6:33:29 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:

353e82

Parents:

458447 (diff), e588312 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'StructureRefactoring' into stable

Conflicts:

src/Actions/AtomAction/AddAction.cpp
src/Actions/AtomAction/ChangeElementAction.cpp
src/Parser/XyzParser.cpp
src/analysis_correlation.cpp
src/atom.cpp
src/config.cpp
src/molecule.cpp

• AtomInfo::element were privatized in stable and element::symbol, ::name in StructureRefactoring (overlapped in various lines).

Location:

src/Actions

Files:

• AnalysisAction/PairCorrelationAction.cpp (modified) (1 diff)
• AnalysisAction/PointCorrelationAction.cpp (modified) (2 diffs)
• AnalysisAction/SurfaceCorrelationAction.cpp (modified) (1 diff)
• AtomAction/AddAction.cpp (modified) (2 diffs)
• AtomAction/ChangeElementAction.cpp (modified) (2 diffs)
• MapOfActions.cpp (modified) (8 diffs)
• MapOfActions.hpp (modified) (2 diffs)

src/Actions/AnalysisAction/PairCorrelationAction.cpp

@@ -75 +75 @@
   ofstream output;
   ofstream binoutput;
-  std::vector< element *> elements;
+  std::vector<const element *> elements;
   string type;
   Vector Point;

src/Actions/AnalysisAction/PointCorrelationAction.cpp

@@ -76 +76 @@
   ofstream output;
   ofstream binoutput;
-  std::vector< element *> elements;
+  std::vector<const element *> elements;
   string type;
   Vector Point;
@@ -96 +96 @@
   cout << "Point to correlate to is  " << Point << endl;
   CorrelationToPointMap *correlationmap = NULL;
-  for(std::vector< element *>::iterator iter = elements.begin(); iter != elements.end(); ++iter)
-    cout << "element is " << (*iter)->symbol << endl;
+  for(std::vector<const element *>::iterator iter = elements.begin(); iter != elements.end(); ++iter)
+    cout << "element is " << (*iter)->getSymbol() << endl;
   std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
   if (periodic)

src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

@@ -79 +79 @@
   ofstream output;
   ofstream binoutput;
-  std::vector< element *> elements;
+  std::vector<const element *> elements;
   string type;
   Vector Point;

src/Actions/AtomAction/AddAction.cpp

@@ -52 +52 @@
 
 Action::state_ptr AtomAddAction::performCall() {
-  element * elemental = NULL;
+  const element * elemental = NULL;
   Vector position;
 
@@ -63 +63 @@
   first->setType(elemental);
   first->setPosition(position);
-  DoLog(1) && (Log() << Verbose(1) << "Adding new atom with element " << first->getType()->name << " at " << (first->getPosition()) << "." << endl);
+  DoLog(1) && (Log() << Verbose(1) << "Adding new atom with element " << first->getType()->getName() << " at " << (first->getPosition()) << "." << endl);
   // TODO: remove when all of World's atoms are stored.
   std::vector<molecule *> molecules = World::getInstance().getAllMolecules();

src/Actions/AtomAction/ChangeElementAction.cpp

@@ -51 +51 @@
 Action::state_ptr AtomChangeElementAction::performCall() {
   atom *first = NULL;
-  element *elemental = NULL;
+  const element *elemental;
   molecule *mol = NULL;
 
@@ -58 +58 @@
   for (World::AtomSelectionIterator iter = World::getInstance().beginAtomSelection(); iter != World::getInstance().endAtomSelection(); ++iter) {
     first = iter->second;
-    DoLog(1) && (Log() << Verbose(1) << "Changing atom " << *first << " to element " << elemental->symbol << "." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "Changing atom " << *first << " to element " << *elemental << "." << endl);
     mol = first->getMolecule();
     first->removeFromMolecule(); // remove atom

src/Actions/MapOfActions.cpp

@@ -296 +296 @@
 
   // value types for the actions
-  TypeMap["add-atom"] = &typeid(element);
+  TypeMap["add-atom"] = &typeid(const element);
   TypeMap["bond-file"] = &typeid(std::string);
   TypeMap["bond-table"] = &typeid(std::string);
@@ -302 +302 @@
   TypeMap["center-in-box"] = &typeid(BoxValue);
   TypeMap["change-box"] = &typeid(BoxValue);
-  TypeMap["change-element"] = &typeid(element);
+  TypeMap["change-element"] = &typeid(const element);
   TypeMap["change-molname"] = &typeid(std::string);
   TypeMap["convex-envelope"] = &typeid(void);
@@ -348 +348 @@
   TypeMap["distances"] = &typeid(VectorValue);
   TypeMap["DoRotate"] = &typeid(bool);
-  TypeMap["element"] = &typeid(element);
-  TypeMap["elements"] = &typeid(std::vector<element *>);
+  TypeMap["element"] = &typeid(const element);
+  TypeMap["elements"] = &typeid(std::vector<const element *>);
   TypeMap["end-step"] = &typeid(int);
   TypeMap["id-mapping"] = &typeid(bool);
@@ -386 +386 @@
   TypeEnumMap[&typeid(atom)] = Atom;
   TypeEnumMap[&typeid(std::vector<atom *>)] = ListOfAtoms;
-  TypeEnumMap[&typeid(element)] = Element;
-  TypeEnumMap[&typeid(std::vector<element *>)] = ListOfElements;
+  TypeEnumMap[&typeid(const element)] = Element;
+  TypeEnumMap[&typeid(std::vector<const element *>)] = ListOfElements;
 
   // default values for any action that needs one (always string!)
@@ -568 +568 @@
 }
 
-void MapOfActions::queryCurrentValue(const char * name, class element * &_T)  {
+void MapOfActions::queryCurrentValue(const char * name, const element * &_T)  {
   int Z = -1;
-  if (typeid( element ) == *TypeMap[name]) {
+  if (typeid(const element ) == *TypeMap[name]) {
     if (CurrentValue.find(name) == CurrentValue.end())
       throw MissingValueException(__FILE__, __LINE__);
@@ -652 +652 @@
 }
 
-void MapOfActions::queryCurrentValue(const char * name, std::vector<element *>&_T)
+void MapOfActions::queryCurrentValue(const char * name, std::vector<const element *>&_T)
 {
   int Z = -1;
-  element *elemental = NULL;
-  if (typeid( std::vector<element *> ) == *TypeMap[name]) {
+  const element *elemental = NULL;
+  if (typeid( std::vector<const element *> ) == *TypeMap[name]) {
     if (CurrentValue.find(name) == CurrentValue.end())
       throw MissingValueException(__FILE__, __LINE__);
@@ -704 +704 @@
 }
 
-void MapOfActions::setCurrentValue(const char * name, class element * &_T)
-{
-  if (typeid( element ) == *TypeMap[name]) {
+void MapOfActions::setCurrentValue(const char * name, const element * &_T)
+{
+  if (typeid(const element ) == *TypeMap[name]) {
     std::ostringstream stream;
     stream << _T->Z;
@@ -764 +764 @@
 }
 
-void MapOfActions::setCurrentValue(const char * name, std::vector<element *>&_T)
-{
-  if (typeid( std::vector<element *> ) == *TypeMap[name]) {
+void MapOfActions::setCurrentValue(const char * name, std::vector<const element *>&_T)
+{
+  if (typeid( std::vector<const element *> ) == *TypeMap[name]) {
     std::ostringstream stream;
-    for (std::vector<element *>::iterator iter = _T.begin(); iter != _T.end(); ++iter) {
+    for (std::vector<const element *>::iterator iter = _T.begin(); iter != _T.end(); ++iter) {
       stream << (*iter)->Z << " ";
     }

src/Actions/MapOfActions.hpp

@@ -164 +164 @@
 
   void queryCurrentValue(const char * name, class atom * &_T);
-  void queryCurrentValue(const char * name, class element * &_T);
+  void queryCurrentValue(const char * name, const element * &_T);
   void queryCurrentValue(const char * name, class molecule * &_T);
   void queryCurrentValue(const char * name, class Box &_T);
   void queryCurrentValue(const char * name, class Vector &_T);
   void queryCurrentValue(const char * name, std::vector<atom *>&_T);
-  void queryCurrentValue(const char * name, std::vector<element *>&_T);
+  void queryCurrentValue(const char * name, std::vector<const element *>&_T);
   void queryCurrentValue(const char * name, std::vector<molecule *>&_T);
   template<typename T> void queryCurrentValue(const char * name, T &_T)
@@ -198 +198 @@
 
   void setCurrentValue(const char * name, class atom * &_T);
-  void setCurrentValue(const char * name, class element * &_T);
+  void setCurrentValue(const char * name, const element * &_T);
   void setCurrentValue(const char * name, class molecule * &_T);
   void setCurrentValue(const char * name, class Box &_T);
   void setCurrentValue(const char * name, class Vector &_T);
   void setCurrentValue(const char * name, std::vector<atom *>&_T);
-  void setCurrentValue(const char * name, std::vector<element *>&_T);
+  void setCurrentValue(const char * name, std::vector<const element *>&_T);
   void setCurrentValue(const char * name, std::vector<molecule *>&_T);
   template<class T> void setCurrentValue(const char * name, T &_T)