Ignore:
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).
File:
1 edited

Legend:

Unmodified
Added
Removed
  • src/Actions/MapOfActions.cpp

    r458447 rb5c53d  
    296296
    297297  // value types for the actions
    298   TypeMap["add-atom"] = &typeid(element);
     298  TypeMap["add-atom"] = &typeid(const element);
    299299  TypeMap["bond-file"] = &typeid(std::string);
    300300  TypeMap["bond-table"] = &typeid(std::string);
     
    302302  TypeMap["center-in-box"] = &typeid(BoxValue);
    303303  TypeMap["change-box"] = &typeid(BoxValue);
    304   TypeMap["change-element"] = &typeid(element);
     304  TypeMap["change-element"] = &typeid(const element);
    305305  TypeMap["change-molname"] = &typeid(std::string);
    306306  TypeMap["convex-envelope"] = &typeid(void);
     
    348348  TypeMap["distances"] = &typeid(VectorValue);
    349349  TypeMap["DoRotate"] = &typeid(bool);
    350   TypeMap["element"] = &typeid(element);
    351   TypeMap["elements"] = &typeid(std::vector<element *>);
     350  TypeMap["element"] = &typeid(const element);
     351  TypeMap["elements"] = &typeid(std::vector<const element *>);
    352352  TypeMap["end-step"] = &typeid(int);
    353353  TypeMap["id-mapping"] = &typeid(bool);
     
    386386  TypeEnumMap[&typeid(atom)] = Atom;
    387387  TypeEnumMap[&typeid(std::vector<atom *>)] = ListOfAtoms;
    388   TypeEnumMap[&typeid(element)] = Element;
    389   TypeEnumMap[&typeid(std::vector<element *>)] = ListOfElements;
     388  TypeEnumMap[&typeid(const element)] = Element;
     389  TypeEnumMap[&typeid(std::vector<const element *>)] = ListOfElements;
    390390
    391391  // default values for any action that needs one (always string!)
     
    568568}
    569569
    570 void MapOfActions::queryCurrentValue(const char * name, class element * &_T)  {
     570void MapOfActions::queryCurrentValue(const char * name, const element * &_T)  {
    571571  int Z = -1;
    572   if (typeid( element ) == *TypeMap[name]) {
     572  if (typeid(const element ) == *TypeMap[name]) {
    573573    if (CurrentValue.find(name) == CurrentValue.end())
    574574      throw MissingValueException(__FILE__, __LINE__);
     
    652652}
    653653
    654 void MapOfActions::queryCurrentValue(const char * name, std::vector<element *>&_T)
     654void MapOfActions::queryCurrentValue(const char * name, std::vector<const element *>&_T)
    655655{
    656656  int Z = -1;
    657   element *elemental = NULL;
    658   if (typeid( std::vector<element *> ) == *TypeMap[name]) {
     657  const element *elemental = NULL;
     658  if (typeid( std::vector<const element *> ) == *TypeMap[name]) {
    659659    if (CurrentValue.find(name) == CurrentValue.end())
    660660      throw MissingValueException(__FILE__, __LINE__);
     
    704704}
    705705
    706 void MapOfActions::setCurrentValue(const char * name, class element * &_T)
    707 {
    708   if (typeid( element ) == *TypeMap[name]) {
     706void MapOfActions::setCurrentValue(const char * name, const element * &_T)
     707{
     708  if (typeid(const element ) == *TypeMap[name]) {
    709709    std::ostringstream stream;
    710710    stream << _T->Z;
     
    764764}
    765765
    766 void MapOfActions::setCurrentValue(const char * name, std::vector<element *>&_T)
    767 {
    768   if (typeid( std::vector<element *> ) == *TypeMap[name]) {
     766void MapOfActions::setCurrentValue(const char * name, std::vector<const element *>&_T)
     767{
     768  if (typeid( std::vector<const element *> ) == *TypeMap[name]) {
    769769    std::ostringstream stream;
    770     for (std::vector<element *>::iterator iter = _T.begin(); iter != _T.end(); ++iter) {
     770    for (std::vector<const element *>::iterator iter = _T.begin(); iter != _T.end(); ++iter) {
    771771      stream << (*iter)->Z << " ";
    772772    }
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