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 a19b4f was             560bbe, checked in by Frederik Heber <heber@…>, 14 years ago | 
        
          | 
AtomicInfo now also (re)stores ParticleInfo::Nr, molecule has own IdPool.
 molecule now also has an internal IdPool to be able to hand out unique ids,
according to uniqueId policy.
new functions: molecule::changeAtomNr(), molecule::setAtomName()
molecule::erase() and ::insert() release and set the id (and the name).
molecule::setAtomName() uses getNr() with id increased by one.
AtomicInfo stores and sets ParticleInfo::Nr.
atom::changeNr() is similar to changeId() only for the molecule.
molecule::AddAtom() does not set the name anymore, is done by ::insert().
simplified molecule::doCountAtoms() a lot, no more naming of atoms.
SPEEDUP: This speeds up the GUI already a lot.
TESTFIX: changed regression test Tesselation/BigNonConvex due to different
ordering of node ids (due to above), surface is still the same (checked).
 | 
        
          | 
              
Property                 mode
 set to                 100644 | 
        
          | File size:
            2.2 KB | 
      
      
| Rev | Line |  | 
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| [bcf653] | 1 | /* | 
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|  | 2 | * Project: MoleCuilder | 
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|  | 3 | * Description: creates and alters molecular systems | 
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| [0aa122] | 4 | * Copyright (C)  2010-2012 University of Bonn. All rights reserved. | 
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| [bcf653] | 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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| [e41c48] | 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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| [d2b28f] | 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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| [ad011c] | 20 | #include "CodePatterns/MemDebug.hpp" | 
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| [d2b28f] | 21 |  | 
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| [e41c48] | 22 | #include "atom.hpp" | 
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|  | 23 | #include "AtomicInfo.hpp" | 
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| [3867a7] | 24 | #include "Descriptors/AtomIdDescriptor.hpp" | 
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|  | 25 | #include "Descriptors/MoleculeIdDescriptor.hpp" | 
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| [3bdb6d] | 26 | #include "Element/element.hpp" | 
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| [e41c48] | 27 | #include "LinearAlgebra/Vector.hpp" | 
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| [3867a7] | 28 | #include "molecule.hpp" | 
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|  | 29 | #include "World.hpp" | 
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| [e41c48] | 30 |  | 
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|  | 31 | /********************************** Functions for class AtomicInfo **********************************/ | 
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|  | 32 |  | 
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|  | 33 | AtomicInfo::AtomicInfo() : | 
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|  | 34 | Type(NULL), | 
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| [3867a7] | 35 | FatherId(0), | 
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|  | 36 | MolId(0), | 
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| [560bbe] | 37 | Id(0), | 
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|  | 38 | Nr(0) | 
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| [e41c48] | 39 | {} | 
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|  | 40 | AtomicInfo::AtomicInfo(const atom &_atom) : | 
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|  | 41 | Position(_atom.getPosition()), | 
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|  | 42 | Type(_atom.getType()), | 
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| [bce72c] | 43 | Velocity(_atom.getAtomicVelocity()), | 
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| [3867a7] | 44 | FatherId(_atom.father->getId()), | 
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|  | 45 | MolId(_atom.getMolecule()->getId()), | 
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| [560bbe] | 46 | Id(_atom.getId()), | 
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|  | 47 | Nr(_atom.getNr()) | 
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| [e41c48] | 48 | {} | 
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|  | 49 |  | 
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|  | 50 | AtomicInfo::~AtomicInfo() | 
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|  | 51 | {} | 
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|  | 52 |  | 
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|  | 53 |  | 
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|  | 54 | bool AtomicInfo::setAtom(atom &_atom) const | 
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|  | 55 | { | 
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|  | 56 | _atom.setPosition(Position); | 
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|  | 57 | _atom.setType(Type); | 
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| [bce72c] | 58 | _atom.setAtomicVelocity(Velocity); | 
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| [3867a7] | 59 |  | 
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|  | 60 | // set old id | 
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|  | 61 | bool status = true; | 
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|  | 62 | if (_atom.getId() != Id) | 
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|  | 63 | status = _atom.changeId(Id); | 
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|  | 64 |  | 
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|  | 65 | // set its father | 
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|  | 66 | atom * const _father = World::getInstance().getAtom(AtomById(FatherId)); | 
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|  | 67 | if (_father == NULL) | 
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|  | 68 | _atom.father = &_atom; | 
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| [e41c48] | 69 | else | 
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| [3867a7] | 70 | _atom.father = _father; | 
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|  | 71 |  | 
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|  | 72 | // setting molecule | 
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|  | 73 | molecule * const _mol = World::getInstance().getMolecule(MoleculeById(MolId)); | 
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|  | 74 | if (_mol != NULL) | 
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|  | 75 | _atom.setMolecule(_mol); // this is ok, mol is const within AtomicInfo, but not outside (atoms need to register) | 
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| [560bbe] | 76 | _atom.changeNr(Nr); | 
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| [3867a7] | 77 |  | 
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|  | 78 | return status; | 
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| [e41c48] | 79 | } | 
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|  | 80 |  | 
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|  | 81 | atomId_t AtomicInfo::getId() const { | 
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|  | 82 | return Id; | 
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|  | 83 | } | 
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|  | 84 |  | 
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|  | 85 | AtomicInfo& AtomicInfo::operator=(const AtomicInfo& AI) | 
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|  | 86 | { | 
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|  | 87 | if (&AI == this)  // check self-assignment | 
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|  | 88 | return *this; | 
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|  | 89 | Position = AI.Position; | 
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|  | 90 | Type = AI.Type; | 
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| [3867a7] | 91 | FatherId = AI.FatherId; | 
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|  | 92 | MolId = AI.MolId; | 
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| [e41c48] | 93 | Velocity = AI.Velocity; | 
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|  | 94 | Id = AI.Id; | 
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| [560bbe] | 95 | Nr = AI.Nr; | 
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| [e41c48] | 96 | return *this; | 
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|  | 97 | } | 
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|  | 98 |  | 
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