source: src/AtomSet.hpp@ 2d292d

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
Last change on this file since 2d292d was 8f4df1, checked in by Frederik Heber <heber@…>, 14 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
File size: 1.9 KB
Line 
1/*
2 * AtomSet.hpp
3 *
4 * Created on: Jul 30, 2010
5 * Author: crueger
6 */
7
8#ifndef ATOMSET_HPP_
9#define ATOMSET_HPP_
10
11
12#include <functional>
13#include <algorithm>
14#include <boost/foreach.hpp>
15#include <limits>
16
17/**
18 * A simple mixin to give any STL conforming structure fast Vector abilities
19 *
20 * TODO: make this work for maps
21 */
22
23#include "atom.hpp"
24#include <list>
25
26// this tests, whether we actually have a Vector
27template <class V>
28struct is_atom{};
29
30template <>
31struct is_atom<atom*>{
32 typedef void wrong_type;
33};
34
35template <class Set>
36class AtomSetMixin : public Set
37{
38 // when our set carries something besides a atom* this will produce an error
39 typedef typename is_atom<typename Set::value_type>::wrong_type check_for_atom;
40public:
41 // typedefs for STL conforming structure
42 typedef typename Set::iterator iterator;
43 typedef typename Set::const_iterator const_iterator;
44
45 AtomSetMixin() :
46 Set()
47 {}
48
49 AtomSetMixin(const Set& src) :
50 Set(src)
51 {}
52 virtual ~AtomSetMixin(){}
53
54 /**
55 * translate all Atoms within this set by a specified amount
56 */
57 void translate(const Vector &translater);
58
59 template<class Function>
60 void transformNodes(Function f);
61
62private:
63 template<class Function>
64 struct workOnNodePointer {
65 workOnNodePointer(Function &_f) : f(_f){}
66 void operator()(atom *atom){
67 atom->setPosition(f(atom->getPosition()));
68 }
69 Function &f;
70 };
71};
72
73template<class Set>
74inline void AtomSetMixin<Set>::translate(const Vector &translater){
75 BOOST_FOREACH(atom *atom,*this){
76 *(atom) += translater;
77 }
78}
79
80template<class Set>
81template<class Function>
82inline void AtomSetMixin<Set>::transformNodes(Function f){
83 std::for_each(this->begin(),
84 this->end(),
85 AtomSetMixin::workOnNodePointer<Function>(f));
86}
87
88// allows simpler definition of AtomSets
89#define ATOMSET(container_type) AtomSetMixin<container_type<atom*> >
90
91#endif /* ATOMSET_HPP_ */
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