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