Changeset 750cff for src/documentation/mainpage.dox

Timestamp:

Oct 31, 2011, 5:13:52 PM (13 years ago)

Author:

Frederik Heber <heber@…>

Branches:

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

Children:

5982c5

Parents:

19bc74

Message:

HUGE: Update on documenation.

• a general skeleton of the documentation is now in place with all the major components of MoleCuilder explained to some extent.
• some information has been transfered from TRAC (e.g. install procecure) into this doxygen documentation where it is general and not specific to the situation at our institute.

File:

• src/documentation/mainpage.dox (modified) (1 diff)

src/documentation/mainpage.dox

@@ -22 +22 @@
  */
 
-/*! \mainpage MoleCuilder - a molecular set builder
+/** \mainpage MoleCuilder - a molecular set builder
  *
- * This introductory shall briefly make acquainted with the program, helping in installing and a first run.
+ * This is the main page of the Doxygen documentation of \e MoleCuilder. We give
+ * a brief description what the program is intended to do and then branch via
+ * the contents of this documentation into various topics.
  *
  * \section about About the Program
  *
- *  MoleCuilder is a program, written entirely in C++, that enables the construction of a coordinate set for the
- *  atoms making up an molecule. It allows for both building of simple molecules by adding atom-wise giving bond
- *  angles and distances or absolute coordinates, but also using them as templates. Regions can be specified and
- *  ordered to be filled with a molecule in a certain manner. Greater conglomerations of molecules can be tesselated
- *  and recognized as a region themselves to be subsequently surrounded by other (surface solvated) molecules.
- *  In the end, MoleCuilder allows the construction of arbitrary nano structures, whether they be crystalline or
- *  amorphic in nature.
+ *  MoleCuilder is a program, written entirely in C++, that enables the
+ *  construction of a coordinate set for the atoms making up an molecule. It
+ *  allows for both building of simple molecules by adding atom-wise giving bond
+ *  angles and distances or absolute coordinates, but also using them as
+ *  templates. Regions can be specified and ordered to be filled with a molecule
+ *  in a certain manner. Greater conglomerations of molecules can be tesselated
+ *  and recognized as a region themselves to be subsequently surrounded by other
+ *  (surface solvated) molecules. In the end, MoleCuilder allows the construction
+ *  of arbitrary nano structures, whether they be crystalline or amorphic in
+ *  nature.
  *
- *  For copyright see \subpage copyright.
+ *  For copyright see \ref copyright.
  *
- * \section Contents
+ * \section idea The central idea behind the program
+ *
+ * What are the central ideas?
+ *
+ * - Testedness: See \ref tests-policy which is meant \e seriously. Nothing is
+ *   worse than one version behaving different to the next with respect to
+ *   output.
+ * - Re-usability: Every piece of functionality should be easy to re-use at
+ *   someplace else. Say no to specialized one-purpose scripts, say yes to
+ *   a LEGO-like system of building your world.
+ * - Extendability: It's easy to add a new piece to the code. And it is even
+ *   more so, if you have read this documentation and know what's all already
+ *   in place.
+ * - Userfriendliness: Every Action can be undone, every Action gives lots
+ *   of output (if desired) to tell you what's going on. It's easy to save
+ *   files in between. There are also three kinds of GUIs, each of which
+ *   have the same functionality.
+ *
+ * \section contents Contents
  *
  * This manual is divided into the following sections:
- * \li \subpage install "Installation Instructions"
- * \li \subpage test "Automated testing"
- * \li \subpage launch "Launching the Code"
- * \li \subpage code "How to the use and extend the code"
+ * \li \ref install
+ * \li \ref tests
+ * \li \ref launch
+ * \li \ref debug
+ * \li \ref code
+ * \li \ref fileformats
+ *
+ * \date 2011-10-31
  *
  */