source: src/Atom/atom_bondedparticle.hpp@ d5b458

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 d5b458 was 7d82a5, checked in by Frederik Heber <heber@…>, 13 years ago

Changed bond::ptr into boost::shared_ptr.

Changes:

  • refactored some BondedParticle functions, cleaning up the interface in terms of private and public functionality, added some helper functions to find bonds.
  • ptr = NULL --> .reset().
  • now initialising to NULL.
  • BondsPerSP is now list of boost::shared_ptr as well.
  • some include of bond.hpp instead of forward references necessary.
  • leftatom and rightatom are now set to NULL on UnregisterBond().
  • bonds are not deleted anymore but simply unregistered.
  • FIX: BondedParticleInfo did unrequiredly inherit AtomObservable.
  • removed UnregisterAllBonds(), code is now in RemoveAllBonds() where UnregisterBond is called for both bond partners. This ensures that the bond is correctly released and shared_ptr free'd.
  • Property mode set to 100644
File size: 2.1 KB
RevLine 
[6b919f8]1/*
2 * atom_bondedparticle.hpp
3 *
4 * Created on: Oct 19, 2009
5 * Author: heber
6 */
7
8#ifndef ATOM_BONDEDPARTICLE_HPP_
9#define ATOM_BONDEDPARTICLE_HPP_
10
11
12using namespace std;
13
14/*********************************************** includes ***********************************/
15
16// include config.h
17#ifdef HAVE_CONFIG_H
18#include <config.h>
19#endif
20
21#include <fstream>
22#include <list>
23
24#include "atom_atominfo.hpp"
25#include "atom_bondedparticleinfo.hpp"
[7d82a5]26#include "atom_observable.hpp"
[6b919f8]27#include "atom_particleinfo.hpp"
[7d82a5]28#include "atom_observable.hpp"
[6b919f8]29
30/****************************************** forward declarations *****************************/
31
32class bond;
33
34/********************************************** declarations *******************************/
35
[7d82a5]36class BondedParticle :
37 public BondedParticleInfo,
38 public virtual ParticleInfo,
39 public virtual AtomInfo,
40 public virtual AtomObservable
41{
[6b919f8]42public:
43 BondedParticle();
44 virtual ~BondedParticle();
45
[88c8ec]46 bond::ptr const addBond(const unsigned int _step, BondedParticle* Partner);
[f63e41]47 void removeBond(const unsigned int _step, BondedParticle* Partner);
[7d82a5]48 void removeBond(bond::ptr &binder);
[5e2f80]49 void removeAllBonds();
[cc9119]50 void removeAllBonds(const unsigned int _step);
[073a9e4]51 bool IsBondedTo(const unsigned int _step, BondedParticle * const BondPartner) const;
[583081]52 void ClearBondsAtStep(const unsigned int _step);
[6b919f8]53 int CountBonds() const;
[e138de]54 int CorrectBondDegree();
[5e2f80]55 void resetBondDegree();
[4b5cf8]56 void OutputBondOfAtom(std::ostream &ost) const;
[1f1b23]57 void OutputBonds(ofstream * const BondFile) const;
[b453f9]58 void OutputOrder(ofstream *file) const;
[6b919f8]59
[d74077]60 std::ostream & operator << (std::ostream &ost) const;
61
[db7e6d]62protected:
[88c8ec]63 bool RegisterBond(const unsigned int _step, bond::ptr const Binder);
[7d82a5]64 bool UnregisterBond(const unsigned int _step, bond::ptr const Binder);
[db7e6d]65
[88c8ec]66 int ContainsBondAtStep(bond::ptr Binder) const;
[6b919f8]67
[7d82a5]68private:
69 unsigned int findBondsStep(bond::ptr const Binder) const;
70 BondList::const_iterator findBondPartnerAtStep(
71 const unsigned int _step,
72 BondedParticle * const Partner) const;
[6b919f8]73};
74
[d74077]75std::ostream & operator << (std::ostream &ost, const BondedParticle &a);
[6b919f8]76
77#endif /* ATOM_BONDEDPARTICLE_HPP_ */
Note: See TracBrowser for help on using the repository browser.