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 71d81a was             6f0841, checked in by Frederik Heber <heber@…>, 14 years ago           | 
        
        
          | 
             
Shifted all modules related to atoms into own subfolder src/Atom/ 
 
- also created own convenience library for this. This makes unit testing on
list containing TesselPoint or atom a lot easier.
 - shifted TesselPoint to src/Atom from src/Tesselation and adapted include's.
  
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| 1 | /*
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| 2 |  * Project: MoleCuilder
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| 3 |  * Description: creates and alters molecular systems
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| 4 |  * Copyright (C)  2010-2011 University of Bonn. All rights reserved.
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| 5 |  * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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| 6 |  */
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| 7 | 
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| 8 | /*
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| 9 |  * AtomicInfo.cpp
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| 10 |  *
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| 11 |  *  Created on: Aug 10, 2010
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| 12 |  *      Author: heber
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| 13 |  */
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| 14 | 
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| 15 | // include config.h
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| 16 | #ifdef HAVE_CONFIG_H
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| 17 | #include <config.h>
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| 18 | #endif
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| 19 | 
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| 20 | #include "CodePatterns/MemDebug.hpp"
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| 21 | 
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| 22 | #include "atom.hpp"
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| 23 | #include "AtomicInfo.hpp"
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| 24 | #include "Element/element.hpp"
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| 25 | #include "LinearAlgebra/Vector.hpp"
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| 26 | 
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| 27 | /********************************** Functions for class AtomicInfo **********************************/
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| 28 | 
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| 29 | AtomicInfo::AtomicInfo() :
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| 30 |     Type(NULL),
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| 31 |     Father(NULL),
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| 32 |     Id(-1)
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| 33 | {}
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| 34 | AtomicInfo::AtomicInfo(const atom &_atom) :
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| 35 |     Position(_atom.getPosition()),
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| 36 |     Type(_atom.getType()),
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| 37 |     Velocity(_atom.getAtomicVelocity()),
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| 38 |     Father(_atom.father),
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| 39 |     Mol(_atom.getMolecule()),
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| 40 |     Id(_atom.getId())
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| 41 | {}
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| 42 | 
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| 43 | AtomicInfo::~AtomicInfo()
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| 44 | {}
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| 45 | 
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| 46 | 
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| 47 | bool AtomicInfo::setAtom(atom &_atom) const
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| 48 | {
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| 49 |   _atom.setPosition(Position);
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| 50 |   _atom.setType(Type);
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| 51 |   _atom.father = const_cast<atom *>(Father); // TODO: Actually, atom::father should be const atom *!
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| 52 |   _atom.setMolecule(const_cast<molecule *>(Mol)); // this is ok, mol is const within AtomicInfo, but not outside (atoms need to register)
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| 53 |   _atom.setAtomicVelocity(Velocity);
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| 54 |   if (_atom.getId() == Id)
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| 55 |     return true;
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| 56 |   else
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| 57 |     return (_atom.changeId(Id));
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| 58 | }
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| 59 | 
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| 60 | atomId_t AtomicInfo::getId() const {
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| 61 |   return Id;
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| 62 | }
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| 63 | 
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| 64 | AtomicInfo& AtomicInfo::operator=(const AtomicInfo& AI)
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| 65 | {
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| 66 |   if (&AI == this)  // check self-assignment
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| 67 |     return *this;
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| 68 |   Position = AI.Position;
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| 69 |   Type = AI.Type;
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| 70 |   Father = AI.Father;
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| 71 |   Mol = AI.Mol;
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| 72 |   Velocity = AI.Velocity;
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| 73 |   Id = AI.Id;
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| 74 |   return *this;
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| 75 | }
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| 76 | 
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