| 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 filling.dox
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| 10 | *
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| 11 | * Created on: Jan 16, 2012
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| 12 | * Author: heber
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| 13 | */
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| 14 |
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| 15 | /** \page filling Filling a domain
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| 16 | *
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| 17 | * The idea behind filling a domain is to cluster it with a set of \b nodes,
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| 18 | * i.e. a position in space in such a way that e.g. around a node is sufficient
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| 19 | * space to fill in the desired molecule. The logic of generating the nodes
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| 20 | * is responsible to create them in such a way as to allow for dense (or
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| 21 | * whatever specific) filling is desired. However, we must not make it too
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| 22 | * complicated. The generation logic for these nodes should concentrate on
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| 23 | * filling the specific domain (sphere, ellipsoid, cuboid, pyramid, ...)
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| 24 | * in the best possible way.
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| 25 | * Whether each node can be filled is then to be decided by a \b predicate.
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| 26 | *
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| 27 | * The filling routine uses then both to traverse the given nodes and
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| 28 | * evaluate the predicate at each.
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| 29 | *
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| 30 | * Hence, the filling of a domain is abstracted into the following parts:
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| 31 | *
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| 32 | * -# \ref Mesh - node containers
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| 33 | * -# \ref FillPredicate - predicates
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| 34 | * -# \ref Filler - a filling routine which itself requires
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| 35 | * -# \ref Cluster - a set of atoms alone(!) inside a specific Shape
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| 36 | * -# \ref CopyAtomsInterface - copy Method for atoms used by Cluster::clone
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| 37 | * -# \ref Inserter - an insertion routine for the cloned cluster
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| 38 | *
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| 39 | * \section filling-node-generation Node generation
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| 40 | *
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| 41 | * The node generation is basically just a point or mesh generator that fills
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| 42 | * a specified region based on the class Shape with a mesh in such a way as to
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| 43 | * fulfill certain criteria:
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| 44 | *
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| 45 | * -# equidistant
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| 46 | * -# containing certain primitive volumes (e.g. for fitting polymers)
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| 47 | * -# ...
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| 48 | *
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| 49 | * \section filling-predicate Predicates
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| 50 | *
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| 51 | * The Predicate pattern has already been used with Descriptors and Shapes.
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| 52 | * These are simply function objects that return a boolean value. I.e. they
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| 53 | * decide whether the current node in the mesh is vacant and can be filled or
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| 54 | * not. As with the predicate() function in the class Descriptor, these should
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| 55 | * be composable via logic operators such as || (or), && (and), ! (not), ...
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| 56 | *
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| 57 | * \note each predicate receives on construction all the required
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| 58 | * information, e.g. LinkedCell_View or Tesselation references or objects, ...
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| 59 | *
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| 60 | * \section filling-filling-routine Filling routine
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| 61 | *
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| 62 | * The filling routine is then simply a function that goes through the given
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| 63 | * number of nodes (completely unaware of the geometry) and evaluates for each
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| 64 | * point the given predicates (which might be a composition of other predicates).
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| 65 | *
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| 66 | * It rejects all nodes that evaluate to false, the list of valid points is
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| 67 | * then traversed again and at each node a Cluster is created by the copy method.
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| 68 | *
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| 69 | * Note that we rely on \ref Cluster's, objects containing a set of atomicId_t
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| 70 | * and a \ref Shape, containing all of these atoms, to fill at each node. We use
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| 71 | * Cluster::clone() to create a copy that is subsequently placed at the desired
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| 72 | * node via an \ref Inserter functor. This allows to either simply shift the
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| 73 | * Cluster or even to perform some random translations and rotations on it, see
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| 74 | * the specific implementations of the class \ref Inserter.
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| 75 | *
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| 76 | *
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| 77 | * \date 2014-03-10
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| 78 | */
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