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 e32fa6 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).
  
           | 
        
        
          
            
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Property                 mode
 set to                 
100644
               
             
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          | 
            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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