Changeset caece4 for src/documentation/mainpage.dox

Timestamp:

May 20, 2014, 9:14:56 AM (11 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:

6029a6

Parents:

74459a

git-author:

Frederik Heber <heber@…> (03/20/14 17:23:35)

git-committer:

Frederik Heber <heber@…> (05/20/14 09:14:56)

Message:

Enhanced documentation significantly.

• went through all of the constructs and updated each.
• enhanced documentation ofr Fragmentation::FragmentMolecule().

File:

• src/documentation/mainpage.dox (modified) (4 diffs)

src/documentation/mainpage.dox

@@ -31 +31 @@
  *
  *  MoleCuilder is a program, written entirely in C++, that enables the
- *  construction of a coordinate set for the atoms making up an molecule. It
+ *  construction of a coordinate set for the atoms making up a molecular system. 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
@@ -37 +37 @@
  *  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.
+ *  (surface solvated) molecules.
+ *  Once initial configurations have been created, empirical potential functions
+ *  can be fitted to ab-initio calculations -- calculated quickly via the BOSSANOVA
+ *  scheme -- to enable subsequent (classical) molecular dynamics simulations.
  *
  *  For copyright see \ref copyright.
@@ -60 +61 @@
  *   files in between. There are also three kinds of GUIs, each of which
  *   have the same functionality.
+ * - Scriptability: Eventually, you want to create lots of configurations with
+ *   only small differences. A session can be stored as either command-line or
+ *   python script and extended to create all of the configurations in a straight-
+ *   forward manner.
  *
  * \section contents Contents
@@ -72 +77 @@
  * \li \ref fileformats
  *
- * \date 2011-10-31
+ * \date 2014-03-10
  *
  */