Changeset 9e1d01 for src/documentation/constructs

Timestamp:

Mar 30, 2012, 9:16:31 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:

b380ed

Parents:

c67ff9

git-author:

Frederik Heber <heber@…> (03/21/12 09:34:00)

git-committer:

Frederik Heber <heber@…> (03/30/12 09:16:31)

Message:

Added CopyAtoms structure.

• this creates a copy of a vector of atoms with as much depth as desired by the user.
• this is a hierarchy of functors that each add additional functionality such as also re-creating the bonds, ...

File:

• src/documentation/constructs/atoms.dox (modified) (1 diff)

src/documentation/constructs/atoms.dox

@@ -56 +56 @@
  * compatible implementation.
  *
+ * \section atoms-copy Copying atoms
  *
- * \date 2011-10-31
+ * Copying atoms is a frequent action. That's why there are specific functors
+ * to get it done in more and more complex ways. The functors all inherit
+ * the \ref CopyAtomsInterface and the more complex ones build upon the
+ * functionality of the simpler ones:
+ * -# CopyAtomsInterface: Internally sets to the number of desired atoms.
+ * -# CopyAtoms_Simple: Fills the internal set with true copies.
+ * -# CopyAtoms_withBonds: Additionally also adds bonds in between the copies
+ *    as they exist in between the original atoms.
+ * -# CopyAtoms_SaturateDanglingBonds: additionally checks for cut bond that
+ *    would now become dangling bonds and inserts additional hydrogens for
+ *    each cut bond such that the copied array of atoms is saturated.
+ *
+ * The CopyAtomsInterface is simple to use:
+ * \code
+ *   std::vector<atom *> atoms_to_copy;
+ *   CopyAtoms_Simple copyMethod;
+ *   copyMethod(atoms_to_copy);
+ *   std::vector<atom *> copiedAtoms = getCopiedAtoms();
+ * \endcode
+ *
+ *
+ * \date 2012-03-30
+ *
  */