| [750cff] | 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 atoms.dox
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| 10 | *
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| 11 | * Created on: Oct 31, 2011
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| 12 | * Author: heber
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| 13 | */
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| 14 |
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| 15 | /**
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| 16 | * \page atoms Atoms
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| 17 | *
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| 18 | * Atoms are the central ingredient. They store the following information:
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| 19 | * - position, velocity, and force (over multiple time steps)
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| 20 | * - element
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| 21 | * - bond neighbours (over multiple time steps)
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| 22 | * - id
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| 23 | *
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| 24 | * \section atoms-structure
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| 25 | *
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| 26 | * The atom class has quite a complicated structure because an atoms has to
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| 27 | * fulfill various roles within this code:
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| 28 | * - atom
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| 29 | * - TesselPoint for Tesselation
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| 30 | * - Graph node for BondGraph
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| 31 | * - bonded particle
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| 32 | *
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| 33 | * There is an onion structure where additional information has been added
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| 34 | * as the layers of an onion via inheritance.
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| 35 | *
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| 36 | * We briefly want to explain the various elements of the inheritance
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| 37 | * - AtomObservable - contains notification channels enumeration and also all
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| 38 | * interface function required by the Observable pattern.
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| 39 | * - AtomInfo - contains position, element and so on.
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| 40 | * - ParticleInfo - contains name and number of the atom
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| 41 | * - BondedParticle - contains all functions related to bonds
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| 42 | * - BondedParticleInfo - contains all member variables related to storing bond
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| 43 | * information
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| 44 | * - GraphNode - contains all functions related to graphs
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| 45 | * - GraphNodeInfo - contains all member variables for graph information
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| 46 | * - TesselPoint - contains functions for considering the atom as a TesselPoint
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| 47 | * in Tesselation (\ref tesselation)
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| 48 | *
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| 49 | * Member variables and functions have been split into class with and without
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| 50 | * added \a ...Info. ...Info classes that are required multiple times are
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| 51 | * inherited as virtual to guarantee that their members are unique (exist
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| 52 | * only once) within an instance.
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| 53 | *
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| 54 | * \note Atoms have a sort-of early serialization concept (\ref serialization)
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| 55 | * as AtomicInfo. \todo This could be refactored into a full serialization
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| 56 | * compatible implementation.
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| 57 | *
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| 58 | *
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| 59 | * \date 2011-10-31
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| 60 | */
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