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
      
      
        
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            Last change
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DOCU: Documentation on ShapeRegistry, QtUI changes, validators, and parameters. 
 
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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 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 |  * \file shapes.dox
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| 10 |  *
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| 11 |  * Created on: Oct 28, 2011
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| 12 |  *    Author: heber
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| 13 |  */
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| 14 | 
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| 15 | /** \page shapes Shapes
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| 16 |  *
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| 17 |  * Shapes are present for denoting a specific region of the simulation domain.
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| 18 |  * There are four primitive types present:
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| 19 |  *  - Sphere
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| 20 |  *  - Ellipsoid
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| 21 |  *  - Cuboid
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| 22 |  *  - Cylinder
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| 23 |  *
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| 24 |  * Note that all may be modified (shrink/grow, rotate, morph) via an arbitrary
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| 25 |  * matrix.
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| 26 |  *
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| 27 |  * The shapes are for the moment only used within \ref descriptors to specify
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| 28 |  * a specific subset of atoms, here that reside in a certain region of the
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| 29 |  * simulation domain.
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| 30 |  *
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| 31 |  * \todo There is a certain relation between Tesselation and Shape. Hence, later
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| 32 |  * Tesselation shall itself be a Shape, i.e. that describes a certain region in
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| 33 |  * space, here via a tesselated mesh.
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| 34 |  *
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| 35 |  * Again, Shapes can be joined via boolean operators:
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| 36 |  * - add
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| 37 |  * - or
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| 38 |  * - not
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| 39 |  *
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| 40 |  * And thus are a very powerful concept.
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| 41 |  *
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| 42 |  * E.g. a shape can be used like this
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| 43 |  * \code
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| 44 |  * Cuboid(Vector(0,0,0), Vector(2,2,2)) && !Sphere(Vector(1,1,1), 1.)
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| 45 |  * \endcode
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| 46 |  * which would match any object within the cuboid from (0,0,0) to (2,2,2)
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| 47 |  * that is not in the unit sphere at (1,1,1).
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| 48 |  *
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| 49 |  *
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| 50 |  * \date 2013-02-07
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| 51 |  *
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| 52 |  */
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