Changeset 0932c2 for src/documentation/constructs

Timestamp:

Jun 27, 2014, 11:43:27 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:

1dbbeb

Parents:

7e3e41

git-author:

Frederik Heber <heber@…> (06/26/14 07:41:59)

git-committer:

Frederik Heber <heber@…> (06/27/14 11:43:27)

Message:

FIX: RandomNumberEngine_Encapsulation::clone() did not set the seed obtained from its prototype.

• this caused all engines to always start with default seed of 1, irrespective of the set parameter. The engine is always cloned from prototypes in the factory that can be manipulated to change their parameters. Hence, clone needs to set the seed (the engine's only parameter).
• EmpiricalPotentials now use RandomNumberGenerator to obtain random starting values.
• TESTFIX: fit-potential regression tests now use fixed seed in order to always take the same amount of time (some test runs in debug mode take very long because of ill-chosen random values).

File:

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

src/documentation/constructs/potentials.dox

@@ -132 +132 @@
  *
  *  As we always start from random initial parameters (within a certain sensible
- *  range at least), the non-linear fit does not always converge. For this case
- *  the FragmentationFitPotentialAction has the option "take-best-of" to allow
- *  for multiple fits where the best (in terms of l2 error) is taken eventually.
+ *  range at least), the non-linear fit does not always converge. Note that the
+ *  random values are drawn from the defined distribution and the uniform distributionm
+ *  engine is obtained from the currently set, see \ref randomnumbers. Hence, you
+ *  can manipulate both in order to get different results or to set the seed such that
+ *  some "randomly" drawn value always work well (e.g. for testing). 
+ *  
+ *  In any case, For this case the FragmentationFitPotentialAction has the option 
+ *  "take-best-of" to allow for multiple fits where the best (in terms of l2 error) 
+ *  is taken eventually. Furthermore, you can use the "set-threshold" option to
+ *  stop restarting the fit procedure first when the L2 error has dropped below the
+ *  given threshold.
  *
  * \section potentials-howto-add Howto add new potentials
@@ -145 +153 @@
  *  -# Add the potential name as case to PotentialFactory such that it knows
  *     how to instantiate your new potential when requested.
+ *  -# Remember to use the the RandomNumberGenerator for getting random starting
+ *     values!
  *
  * PotentialTypes.def contains a boost::preprocessor sequence of all