Changeset 38c5d1 for src/documentation/constructs/linkedcell.dox

Timestamp:

Feb 22, 2012, 11:28:52 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:

040a5c

Parents:

712886

git-author:

Frederik Heber <heber@…> (01/05/12 16:51:58)

git-committer:

Frederik Heber <heber@…> (02/22/12 11:28:52)

Message:

Documentation update on how to use the new linked cell construct.

File:

• src/documentation/constructs/linkedcell.dox (modified) (2 diffs)

src/documentation/constructs/linkedcell.dox

@@ -64 +64 @@
  * The following snippet gives you access to the linked cell interface.
  * \code
- *  LinkedCell_View &interface = World::getInstance().getLinkedCellView();
+    LinkedCell_View &interface = World::getInstance().getLinkedCell(double distance);
  * \endcode
+ * where distance is the desired edge length for the linked cell construct (e.g.
+ * the maximum distance where you want neighbors to be returned).
  *
  * Now, you can access its functions as simply as
  * \code
- *  LinkedList &list = interface.getAllNeighbours(Vector(0.,0.,0.), 4.);
+    LinkedList &list = interface.getAllNeighbours(4., Vector(0.,0.,0.));
  * \endcode
  * which returns a LinkedList, i.e. a set of points, that reside in a sphere
@@ -75 +77 @@
  * current in the Box stored in the World:
  * \code
- * World::getInstance().getDomain()
+   World::getInstance().getDomain()
  * \endcode
  *
+ * You can iterate over the LinkedList as follows:
+ * \code
+    if (!ListOfNeighbors.empty()) {
+      // we have some possible candidates, go through each
+      for (LinkedCell::LinkedList::const_iterator neighboriter = ListOfNeighbors.begin();
+          neighboriter != ListOfNeighbors.end();
+          ++neighboriter) {
+        const atom * const OtherWalker = dynamic_cast<const atom *>(*neighboriter);
+        ASSERT(OtherWalker != NULL,
+            "__func__ - TesselPoint "
+            +(*neighboriter)->getName()+" that was not an atom retrieved from LinkedList");
+         ...
+
+        }
+      }
+ * \endcode
+ * Note that we dynamically cast the TesselPoint to its more involved class atom which is
+ * in general ok as only atoms are contained in LinkedCell constructs.
  *
  * \date 2011-11-30