Changeset caece4 for src/documentation/constructs/filling.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/constructs/filling.dox (modified) (6 diffs)

src/documentation/constructs/filling.dox

@@ -15 +15 @@
 /** \page filling Filling a domain
  *
- * The idea behind filling a domain is to cluster it with a set of nodes,
- * i.e. a position in space in such a way that e.g. around node is sufficient
+ * The idea behind filling a domain is to cluster it with a set of \b nodes,
+ * i.e. a position in space in such a way that e.g. around a node is sufficient
  * space to fill in the desired molecule. The logic of generating the nodes
  * is responsible to create them in such a way as to allow for dense (or
@@ -23 +23 @@
  * filling the specific domain (sphere, ellipsoid, cuboid, pyramid, ...)
  * in the best possible way.
- * Whether each node can be filled is then to be decided by a predicate.
+ * Whether each node can be filled is then to be decided by a \b predicate.
  *
  * The filling routine uses then both to traverse the given nodes and
@@ -40 +40 @@
  *
  * The node generation is basically just a point or mesh generator that fills
- * a specified region (best would be based on the class Shape) with a mesh in
- * such a way as to fulfill certain criteria:
+ * a specified region based on the class Shape with a mesh in such a way as to 
+ * fulfill certain criteria:
  *
  *    -# equidistant
@@ -55 +55 @@
  * be composable via logic operators such as || (or), && (and), ! (not), ...
  *
- * Note that each predicate receives on construction all the required
+ * \note each predicate receives on construction all the required
  * information, e.g. LinkedCell_View or Tesselation references or objects, ...
  *
@@ -65 +65 @@
  *
  * It rejects all nodes that evaluate to false, the list of valid points is
- * then traversed again and at each node a Cluster is created.
+ * then traversed again and at each node a Cluster is created by the copy method.
  *
  * Note that we rely on \ref Cluster's, objects containing a set of atomicId_t
- * and that are inside a contained \ref Shape, to fill at each node. We use
+ * and a \ref Shape, containing all of these atoms, to fill at each node. We use
  * Cluster::clone() to create a copy that is subsequently placed at the desired
  * node via an \ref Inserter functor. This allows to either simply shift the
@@ -75 +75 @@
  *
  *
- * \date 2012-01-16
+ * \date 2014-03-10
  */