source: src/documentation/constructs/fragmentation.dox@ 3aa204

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Last change on this file since 3aa204 was caece4, checked in by Frederik Heber <heber@…>, 11 years ago

Enhanced documentation significantly.

  • went through all of the constructs and updated each.
  • enhanced documentation ofr Fragmentation::FragmentMolecule().
  • Property mode set to 100644
File size: 3.4 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8/**
9 * \file fragmentation.dox
10 *
11 * Created on: Oct 28, 2011
12 * Author: heber
13 */
14
15/** \page fragmentation Fragmentation
16 *
17 * Fragmentation contains all routines that are required to split a given
18 * molecular system into fragments. This is part of the so-called BOSSANOVA
19 * (Bond Order diSSection in an ANOVA-like fashion) approach to get linear
20 * scaling complexity for ab-initio quantum chemistry methods. This method is
21 * explained in the doctoral thesis of Frederik Heber.
22 *
23 * \secton fragmentation-fragmentation Fragmenting molecules
24 *
25 * Everything starts in the Action FragmentationFragmentationAction. We require
26 * a list of selected atoms. These are browsed and we note down all the associated
27 * molecules (fragmentation is molecule-based). Subsequently, we make sure that
28 * the bond degree has correct bond degress with respect to the selected set.
29 * Then, Fragmentation is created for each molecule in the list.
30 * The class Fragmentation contains with Fragmentation::FragmentMolecule()
31 * the main routine that dissect a given molecule
32 * Afterwards, all KeySet's are obtained as a Graph from the Fragmentation
33 * instance and combined into a single graph.
34 * Via a depth first search analysis cycles are detected and added as
35 * cycle fragments to this sets of KeySet.
36 * Finally, all fragments are placed in the FragmentationResultContainer.
37 *
38 * If desired, \b inter-fragments, that fragments are combined if they are only
39 * a certain distance apart from another and their summed fragmentation orders
40 * do not exceed the specified value. This is required for local correlation
41 * calculation. Otherwise correlation is only calculated (if supported by the
42 * solver) within covalently connected fragments, i.e. we do not get any van
43 * der Waals interactions.
44 *
45 * These fragments may be exported to file if output file types \sa fileformats
46 * are given. There, the current FormatParserParameters are used. If none are
47 * given, fragments remain in the FragmentationResultContainer.
48 *
49 * \secton fragmentation-automation Calculating fragments
50 *
51 * If then FragmentationFragmentationAutomationAction is used, these are converted
52 * into MPQCJobs (and VMGJobs) that are passed on via a network connection to a
53 * JobMarket's server as a FragmentJob.
54 * Any idling connected clients will then process each one of the jobs until the
55 * whole bundle is completed. The Action checks on the current tatus of the jobs
56 * and requests any finished jobs (FragmentResult).
57 * After all jobs' results have been received, they are stored in
58 * FragmentationShortRangeResults and FragmentationLongrangeResults.
59 * FragmentationAnalyseFragmentResultsAction will process both these results and
60 * sum up the approximate energy and forces (where these are set as the atoms'
61 * forces for the current time step).
62 *
63 * Alternatively to automation, where everything is done inside MoleCuilder, one
64 * may also use the exported files to calculate an approximation. To this end,
65 * the energies and forces are put together via \b joiner to approximation
66 * to the total energy and forces of the whole molecular system. Later,
67 * \b analyzer additionally gives data on how good this approximation has
68 * worked out in plotable format.
69 *
70 *
71 * \date 2014-03-10
72 *
73 */
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