source: src/documentation/userguide.dox@ 2528d8

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since 2528d8 was 6029a6, checked in by Frederik Heber <heber@…>, 11 years ago

Added largely extended userguide with some images into subfolder of doc folder.
  • Property mode set to 100644
File size: 1.9 KB
RevLine 
[6029a6]1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2014 Frederik Heber. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8/**
9 * \file userguide.dox
10 *
11 * Created on: Apr 18, 2014
12 * Author: heber
13 */
14
15/**
16 * \page userguide How to write the userguide
17 *
18 * The userguide is written with docbook. We have use XXE as means to write
19 * the guide in a WYSIWYG style.
20 *
21 * In general, the guide
22 * http://movementarian.org/docs/docbook-autotools/index.html
23 * has been very helpful in setting docbook usage up with autotools. We
24 * followed it closely with some minor modifications as we want to generate
25 * a pdf instead of html.
26 *
27 * \section userguide-images How to get images working
28 *
29 * We have multiple screenshots to explain the graphical interface. These
30 * reside in a distinct folder pictures. However, to get it working with
31 * autotools we need to change some paths. And there we ran into a lot of
32 * (newbie) trouble with docbook or rather with xsltproc, the preprocessor
33 * for xml files in conjunction with xsl stylesheets.
34 *
35 * At one point we stumbled over catalogs that seem to be able to tell the
36 * processor that he should look elsewhere for certain files but we could
37 * get the processor to actually use these directives.
38 *
39 * Finally, we stumbled on some more and came onto this guide
40 * http://www.sagehill.net/docbookxsl/GraphicsLocations.html
41 * that finally explained what was the point with those images. So, we can
42 * use either \a fileref, which might work if we set \a img.src.path, or we
43 * have to define our images as entities in the very beginning of the xml
44 * document and reference them via \a entityref with just the given token.
45 * The latter then worked with the catalog as these are actually looked up,
46 * i.e. here the URI mechanism does finally work. It does not work in the
47 * case of fileref.
48 *
49 *
50 * \date 2014-04-18
51 *
52 */
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