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 dba7b0 was             2a0271, checked in by Frederik Heber <heber@…>, 14 years ago | 
        
          | 
New function Box::isValid() to be discerned from ::isInside().
 isValid checks with and isInside without boundary conditions.
added Box::isValid() check to LinkedCell_Model::getIndexToVector().
TESTFIX: regression test Atoms/Add needed Ignore BCs.
 | 
        
          | 
              
Property                 mode
 set to                 100644 | 
        
          | File size:
            1.7 KB | 
      
      
| Rev | Line |  | 
|---|
| [2ced6b] | 1 | /* | 
|---|
|  | 2 | * Project: MoleCuilder | 
|---|
|  | 3 | * Description: creates and alters molecular systems | 
|---|
| [0aa122] | 4 | * Copyright (C)  2012 University of Bonn. All rights reserved. | 
|---|
| [2ced6b] | 5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details. | 
|---|
|  | 6 | */ | 
|---|
|  | 7 |  | 
|---|
|  | 8 | /* | 
|---|
|  | 9 | * ObserverBoxStub.cpp | 
|---|
|  | 10 | * | 
|---|
|  | 11 | *  Created on: Dec 22, 2011 | 
|---|
|  | 12 | *      Author: heber | 
|---|
|  | 13 | */ | 
|---|
|  | 14 |  | 
|---|
|  | 15 | // include config.h | 
|---|
|  | 16 | #ifdef HAVE_CONFIG_H | 
|---|
|  | 17 | #include <config.h> | 
|---|
|  | 18 | #endif | 
|---|
|  | 19 |  | 
|---|
|  | 20 | #include "CodePatterns/MemDebug.hpp" | 
|---|
|  | 21 |  | 
|---|
|  | 22 | #include "Box.hpp" | 
|---|
|  | 23 |  | 
|---|
|  | 24 | #include "CodePatterns/Observer/Channels.hpp" | 
|---|
|  | 25 | #include "CodePatterns/Observer/Notification.hpp" | 
|---|
|  | 26 | #include "LinearAlgebra/RealSpaceMatrix.hpp" | 
|---|
|  | 27 |  | 
|---|
|  | 28 |  | 
|---|
|  | 29 | Box::Box(RealSpaceMatrix _M) : | 
|---|
|  | 30 | Observable("Box"), | 
|---|
|  | 31 | M( new RealSpaceMatrix(_M) ), | 
|---|
|  | 32 | Minv( new RealSpaceMatrix ) | 
|---|
|  | 33 | { | 
|---|
|  | 34 | // observable stuff | 
|---|
|  | 35 | Channels *OurChannel = new Channels; | 
|---|
|  | 36 | NotificationChannels.insert( std::make_pair(this, OurChannel) ); | 
|---|
|  | 37 | // add instance for each notification type | 
|---|
|  | 38 | OurChannel->addChannel(Box::MatrixChanged); | 
|---|
|  | 39 | *Minv = M->invert(); | 
|---|
|  | 40 | } | 
|---|
|  | 41 |  | 
|---|
|  | 42 | Box::~Box() | 
|---|
|  | 43 | { | 
|---|
|  | 44 | // observable stuff | 
|---|
|  | 45 | std::map<Observable *, Channels*>::iterator iter = NotificationChannels.find(this); | 
|---|
|  | 46 | delete iter->second; | 
|---|
|  | 47 | NotificationChannels.erase(iter); | 
|---|
|  | 48 |  | 
|---|
|  | 49 | delete M; | 
|---|
|  | 50 | delete Minv; | 
|---|
|  | 51 | } | 
|---|
|  | 52 |  | 
|---|
|  | 53 | const RealSpaceMatrix &Box::getMinv() const | 
|---|
|  | 54 | { | 
|---|
|  | 55 | return *Minv; | 
|---|
|  | 56 | } | 
|---|
|  | 57 |  | 
|---|
| [712886] | 58 | Vector Box::enforceBoundaryConditions(const Vector &point) const{ | 
|---|
| [c52e08] | 59 | return point; | 
|---|
|  | 60 | } | 
|---|
|  | 61 |  | 
|---|
|  | 62 | const BoundaryConditions::Conditions_t & Box::getConditions() const | 
|---|
| [2ced6b] | 63 | { | 
|---|
| [d66cb7] | 64 | return conditions.get(); | 
|---|
| [2ced6b] | 65 | } | 
|---|
|  | 66 |  | 
|---|
| [c52e08] | 67 | double Box::periodicDistanceSquared(const Vector &point1,const Vector &point2) const | 
|---|
|  | 68 | { | 
|---|
|  | 69 | return point1.DistanceSquared(point2); | 
|---|
|  | 70 | } | 
|---|
|  | 71 |  | 
|---|
| [2a0271] | 72 | bool Box::isValid(const Vector &p) const | 
|---|
|  | 73 | { | 
|---|
|  | 74 | return true; | 
|---|
|  | 75 | } | 
|---|
|  | 76 |  | 
|---|
| [69459d] | 77 | void Box::setM(RealSpaceMatrix _M) | 
|---|
|  | 78 | { | 
|---|
|  | 79 | OBSERVE; | 
|---|
|  | 80 | NOTIFY(MatrixChanged); | 
|---|
|  | 81 | delete M; | 
|---|
|  | 82 | M = new RealSpaceMatrix(_M); | 
|---|
|  | 83 | *Minv = M->invert(); | 
|---|
|  | 84 | } | 
|---|
       
      
  Note:
 See   
TracBrowser
 for help on using the repository browser.