Changeset 750cff for src/documentation/launch.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/launch.dox (modified) (1 diff)

src/documentation/launch.dox

@@ -13 +13 @@
  */
 
-/*
- * \subpage launch Running the code
+/**
+ * \page launch Running the code
  *
- *  The program can be executed by running: ./molecuilder
+ *  Before you have done
+ *  \code
+ *  make install
+ *  \endcode
+ *  The executables are in the \b src folder of your build directory. There are
+ *  two variants:
+ *  - molecuilder (contains command line and text interface)
+ *  - molecuildergui (contains graphical user interface)
  *
- *  MoleCuilder has three interfaces at your disposal:
- *  -# Textmenu: A simple interactive console-based menu, where awaits your choices and inputs in order to set atoms
- *               as you like
- *  -# CommandLineUI: Every command can also be chained up as a sequence of actions on the command line to be executed
- *               with any user interaction.
- *  -# GraphicalUI: A graphical user interface that also display the molecular structure being built and lots of other
- *               informations to ease the construction of bigger geometries.
+ *  The programs can be executed by running:
+ *  - Text menu: Launching molecuilder with no options always gives the text menu.
+ *    \code ./molecuilder \endcode
+ *  - Command line menu: Depends on what you want, but an exemplary call is
+ *    \code ./molecuilder -i test.xyz -o tremolo xyz -v 3 --add-atom H --position "0,0,0"\endcode
+ *  - Graphical menu
+ *    \code ./molecuildergui \endcode
  *
- *  The supported output formats right now are:
- *  -# mpqc: Configuration files of the Massively Parallel Quantum Chemistry package (Sandia labs)
- *  -# pcp: Configuration files of the Parallel Car-Parrinello program (Institute for Numerical Simulation)
- *  -# tremolo: Configuration files of TREMOLO (Institute for Numerical Simulation)
- *  -# xyz: the most basic format for the 3d arrangement of atoms consisting of a list of element and 3 coordinates.
+ * The user interface are explained in greater detail in \ref userinterfaces.
  *
- *  \section
+ *
+ * \date 2011-10-31
  *
  */