| 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 | * Copyright (C) 2014 Frederik Heber. All rights reserved.
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| 6 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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| 7 | */
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| 8 |
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| 9 | /**
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| 10 | * \file atoms.dox
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| 11 | *
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| 12 | * Created on: Oct 31, 2011
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| 13 | * Author: heber
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| 14 | */
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| 15 |
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| 16 | /**
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| 17 | * \page atoms Atoms
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| 18 | *
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| 19 | * Atoms are the central ingredient. They store the following information:
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| 20 | * - position, velocity, and force (over multiple time steps)
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| 21 | * - element
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| 22 | * - bond neighbours (over multiple time steps)
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| 23 | * - id
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| 24 | *
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| 25 | * \section atoms-structure
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| 26 | *
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| 27 | * The atom class has quite a complicated structure because an atoms has to
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| 28 | * fulfill various roles within this code:
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| 29 | * - atom
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| 30 | * - TesselPoint for Tesselation
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| 31 | * - Graph node for BondGraph
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| 32 | * - bonded particle
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| 33 | *
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| 34 | * There is an onion structure where additional information has been added
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| 35 | * as the layers of an onion via inheritance.
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| 36 | *
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| 37 | * We briefly want to explain the various elements of the inheritance
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| 38 | * - AtomObservable - contains notification channels enumeration and also all
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| 39 | * interface function required by the Observable pattern.
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| 40 | * - AtomInfo - contains position, element and so on.
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| 41 | * - ParticleInfo - contains name and number of the atom
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| 42 | * - BondedParticle - contains all functions related to bonds
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| 43 | * - BondedParticleInfo - contains all member variables related to storing bond
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| 44 | * information
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| 45 | * - GraphNode - contains all functions related to graphs
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| 46 | * - GraphNodeInfo - contains all member variables for graph information
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| 47 | * - TesselPoint - contains functions for considering the atom as a TesselPoint
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| 48 | * in Tesselation (\ref tesselation)
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| 49 | *
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| 50 | * Member variables and functions have been split into class with and without
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| 51 | * added \a ...Info. ...Info classes that are required multiple times are
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| 52 | * inherited as virtual to guarantee that their members are unique (exist
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| 53 | * only once) within an instance.
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| 54 | *
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| 55 | * \note Atoms have a sort-of early serialization concept (\ref serialization)
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| 56 | * as AtomicInfo. \todo This could be refactored into a full serialization
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| 57 | * compatible implementation.
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| 58 | *
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| 59 | * \section atoms-copy Copying atoms
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| 60 | *
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| 61 | * Copying atoms is a frequent action. That's why there are specific functors
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| 62 | * to get it done in more and more complex ways. The functors all inherit
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| 63 | * the \ref CopyAtomsInterface and the more complex ones build upon the
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| 64 | * functionality of the simpler ones:
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| 65 | * -# CopyAtomsInterface: Internally sets to the number of desired atoms.
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| 66 | * -# CopyAtoms_Simple: Fills the internal set with true copies.
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| 67 | * -# CopyAtoms_withBonds: Additionally also adds bonds in between the copies
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| 68 | * when they exist in between the original atoms.
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| 69 | * -# CopyAtoms_SaturateDanglingBonds: additionally checks for cut bond that
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| 70 | * would now become dangling bonds and inserts additional hydrogens for
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| 71 | * each cut bond such that the copied array of atoms is saturated.
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| 72 | *
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| 73 | * The CopyAtomsInterface is simple to use:
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| 74 | * \code
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| 75 | * std::vector<atom *> atoms_to_copy;
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| 76 | * CopyAtoms_Simple copyMethod;
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| 77 | * copyMethod(atoms_to_copy);
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| 78 | * std::vector<atom *> copiedAtoms = getCopiedAtoms();
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| 79 | * \endcode
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| 80 | *
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| 81 | *
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| 82 | * \date 2012-03-30
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| 83 | *
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| 84 | */
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