Changeset dba7b0

Timestamp:

Mar 30, 2012, 9:18:26 AM (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:

901d87

Parents:

da1e92

git-author:

Frederik Heber <heber@…> (03/21/12 10:20:18)

git-committer:

Frederik Heber <heber@…> (03/30/12 09:18:26)

Message:

Extended filling documentation for Inserter.

File:

• src/documentation/constructs/filling.dox (modified) (4 diffs)

src/documentation/constructs/filling.dox

@@ -23 +23 @@
  * filling the specific domain (sphere, ellipsoid, cuboid, pyramid, ...)
  * in the best possible way.
- * Whether each node can be filled is then to ve decided by a predicate.
+ * Whether each node can be filled is then to be decided by a predicate.
  *
  * The filling routine uses then both to traverse the given nodes and
@@ -30 +30 @@
  * Hence, the filling of a domain is abstracted into the following parts:
  *
- *  -# node generation
- *  -# predicates
- *  -# filling routine
+ *  -# \ref Mesh - node containers
+ *  -# \ref FillPredicate - predicates
+ *  -# \ref Filler - a filling routine which itself requires
+ *    -# \ref Cluster - a set of atoms alone(!) inside a specific Shape
+ *    -# \ref CopyAtomsInterface - copy Method for atoms used by Cluster::clone
+ *    -# \ref Inserter - an insertion routine for the cloned cluster
  *
  * \section filling-node-generation Node generation
@@ -50 +53 @@
  * decide whether the current node in the mesh is vacant and can be filled or
  * not. As with the predicate() function in the class Descriptor, these should
- * be composable via logic operators such as , &&, not, ...
+ * be composable via logic operators such as || (or), && (and), ! (not), ...
  *
  * Note that each predicate receives on construction all the required
@@ -62 +65 @@
  *
  * It rejects all nodes that evaluate to false, the list of valid points is
- * then traversed again and at each node a molecule is created.
+ * then traversed again and at each node a Cluster is created.
  *
+ * 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
+ * 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
+ * Cluster or even to perform some random translations and rotations on it, see
+ * the specific implementations of the class \ref Inserter.
  *
  *