Changeset caece4 for src/documentation/future.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/future.dox (modified) (3 diffs)

src/documentation/future.dox

@@ -20 +20 @@
  * Here is a list of what pieces of the code should be refactored to make them
  * easier to use:
- * - Fragmentation and related classes: Just generate the keysets and have a
- *  pool of hydrogen atoms that are re-used when creating and writing
- *  fragments. Add and re-add messes up the Id's of the Atom's.
  * - Tesselation and related classes: Especially, the removing and adding of
  *  nodes is not fully (and correctly) implemented, see the regression tests
@@ -33 +30 @@
  * Here the list of what should be implemented to make the code more powerful
  * and just makes sense given the current constructs.
- * - LinkedCell should be owned by the World and internally, such that one
- *  simply may access nearest neighbors (e.g. via Selection of a sphere) but in
- * \f$ {\cal O}(N) \f$ and not naively \f${\cal} (N^2)\f$.
- * - LinkedCell should be updateable. Thus it could listen to World's
- *  notifications when World::AtomInserted or World::AtomRemoved and update.
- *  Hence, it would always be up-to-date. Combined with the Cachable pattern in
- *  CodePatterns realizing lazy evaluation (http://en.wikipedia.org/wiki/Lazy_evaluation),
- *  i.e. when many updates have gathered, we rather re-create the linked cell
- *  structure, this can easily be made very convenient, fast, and powerful.
  * - BondGraph should be updataeable. As above it should listen the Worlds'
  *  notifications and so on (also Cachable ...)
@@ -55 +43 @@
  *  new Action but a token that just tells how to fill and a factory pattern
  *  behind it that spits out the algorithm how to do it.
+ * - molecule's should also contain the bounding box. This would allow to use
+ *  them as crystallic unit cells.
  *
  *
- * \date 2011-11-03
+ * \date 2014-03-10
  *
  */