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
        Candidate_v1.7.0
        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
      
      
        
          | 
            Last change
 on this file since 73a857 was             8f4df1, checked in by Frederik Heber <heber@…>, 15 years ago           | 
        
        
          | 
             
Merge branch 'AtomicPositionEncapsulation' into stable 
 
Conflicts: 
 
src/Actions/AtomAction/ChangeElementAction.cpp 
src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp 
src/Makefile.am 
src/UIElements/TextUI/TextDialog.cpp 
src/analysis_correlation.hpp 
src/atom.cpp 
src/atom_atominfo.hpp 
src/bond.cpp 
src/boundary.cpp 
src/molecule_geometry.cpp 
src/tesselation.cpp 
src/tesselationhelpers.cpp 
src/triangleintersectionlist.cpp 
src/unittests/Makefile.am 
 
 
- fixed #includes due to moves to Helpers and LinearAlgebra
 - moved VectorInterface.* and vector_ops.* to LinearAlgebra
 - no more direct access of atom::node, remapped to set/getPosition()
 - no more direct access to atom::type, remapped to set/getType() (also in atom due to
derivation and atominfo::AtomicElement is private not protected).
  
           | 
        
        
          
            
              - 
Property                 mode
 set to                 
100644
               
             
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          | 
            File size:
            1.9 KB
           | 
        
      
      
| Line |   | 
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| 1 | /*
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| 2 |  * AtomSet.hpp
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| 3 |  *
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| 4 |  *  Created on: Jul 30, 2010
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| 5 |  *      Author: crueger
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| 6 |  */
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| 7 | 
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| 8 | #ifndef ATOMSET_HPP_
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| 9 | #define ATOMSET_HPP_
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| 10 | 
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| 11 | 
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| 12 | #include <functional>
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| 13 | #include <algorithm>
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| 14 | #include <boost/foreach.hpp>
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| 15 | #include <limits>
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| 16 | 
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| 17 | /**
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| 18 |  * A simple mixin to give any STL conforming structure fast Vector abilities
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| 19 |  *
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| 20 |  * TODO: make this work for maps
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| 21 |  */
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| 22 | 
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| 23 | #include "atom.hpp"
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| 24 | #include <list>
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| 25 | 
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| 26 | // this tests, whether we actually have a Vector
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| 27 | template <class V>
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| 28 | struct is_atom{};
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| 29 | 
 | 
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| 30 | template <>
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| 31 | struct is_atom<atom*>{
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| 32 |   typedef void wrong_type;
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| 33 | };
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| 34 | 
 | 
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| 35 | template <class Set>
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| 36 | class AtomSetMixin : public Set
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| 37 | {
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| 38 |   // when our set carries something besides a atom* this will produce an error
 | 
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| 39 |   typedef typename is_atom<typename Set::value_type>::wrong_type check_for_atom;
 | 
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| 40 | public:
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| 41 |   // typedefs for STL conforming structure
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| 42 |   typedef typename Set::iterator iterator;
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| 43 |   typedef typename Set::const_iterator const_iterator;
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| 44 | 
 | 
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| 45 |   AtomSetMixin() :
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| 46 |     Set()
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| 47 |   {}
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| 48 | 
 | 
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| 49 |   AtomSetMixin(const Set& src) :
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| 50 |     Set(src)
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| 51 |   {}
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| 52 |   virtual ~AtomSetMixin(){}
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| 53 | 
 | 
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| 54 |   /**
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| 55 |    * translate all Atoms within this set by a specified amount
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| 56 |    */
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| 57 |   void translate(const Vector &translater);
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| 58 | 
 | 
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| 59 |   template<class Function>
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| 60 |   void transformNodes(Function f);
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| 61 | 
 | 
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| 62 | private:
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| 63 |   template<class Function>
 | 
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| 64 |   struct workOnNodePointer {
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| 65 |     workOnNodePointer(Function &_f) : f(_f){}
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| 66 |     void operator()(atom *atom){
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| 67 |       atom->setPosition(f(atom->getPosition()));
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| 68 |     }
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| 69 |     Function &f;
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| 70 |   };
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| 71 | };
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| 72 | 
 | 
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| 73 | template<class Set>
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| 74 | inline void AtomSetMixin<Set>::translate(const Vector &translater){
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| 75 |   BOOST_FOREACH(atom *atom,*this){
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| 76 |     *(atom) += translater;
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| 77 |   }
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| 78 | }
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| 79 | 
 | 
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| 80 | template<class Set>
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| 81 | template<class Function>
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| 82 | inline void AtomSetMixin<Set>::transformNodes(Function f){
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| 83 |   std::for_each(this->begin(),
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| 84 |                 this->end(),
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| 85 |                 AtomSetMixin::workOnNodePointer<Function>(f));
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| 86 | }
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| 87 | 
 | 
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| 88 | // allows simpler definition of AtomSets
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| 89 | #define ATOMSET(container_type) AtomSetMixin<container_type<atom*> >
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| 90 | 
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| 91 | #endif /* ATOMSET_HPP_ */
 | 
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