Changeset 750cff for src/builder.cpp

Timestamp:

Oct 31, 2011, 5:13:52 PM (14 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/builder.cpp (modified) (1 diff)

src/builder.cpp

@@ -13 +13 @@
  */
 
-/*! \page Copyright notice
- *
- *  MoleCuilder - to create and alter molecular systems
- *  Copyright (C) 2010  University Bonn. All rights reserved.
- *
- */
-
-/*! \mainpage MoleCuilder - a molecular set builder
- *
- * This introductory shall briefly make acquainted with the program, helping in installing and a first run.
- *
- * \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.
- *
- *
- * \section install Installation
- *
- *  Installation should without problems succeed as follows:
- *  -# ./configure (or: mkdir build;mkdir run;cd build; ../configure --bindir=../run)
- *  -# make
- *  -# make install
- *
- *  Further useful commands are
- *  -# make clean uninstall: deletes .o-files and removes executable from the given binary directory\n
- *  -# make doxygen-doc: Creates these html pages out of the documented source
- *  -# make check: Runs an extensive set of unit tests and a testsuite which also gives a good overview on the set of
- *                 functions.
- *
- * \section run Running
- *
- *  The program can be executed by running: ./molecuilder
- *
- *  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 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.
- *
- */
 
 // include config.h