Changeset caece4 for src/Fragmentation

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/Fragmentation/Fragmentation.cpp (modified) (2 diffs)

src/Fragmentation/Fragmentation.cpp

@@ -66 +66 @@
 /** Constructor of class Fragmentation.
  *
- * \param _mol molecule for internal use (looking up atoms)
+ * \param _mol molecule which we currently fragment
  * \param _FileChecker instance contains adjacency parsed from elsewhere
  * \param _treatment whether to treat hydrogen special and saturate dangling bonds or not
@@ -84 +84 @@
 
 /** Performs a many-body bond order analysis for a given bond order.
- * -# parses adjacency, keysets and orderatsite files
- * -# RootStack is created for every subgraph (here, later we implement the "update 10 sites with highest energ
-y contribution", and that's why this consciously not done in the following loop)
- * -# in a loop over all subgraphs
- *  -# calls FragmentBOSSANOVA with this RootStack and within the subgraph molecule structure
- *  -# creates molecule (fragment)s from the returned keysets (StoreFragmentFromKeySet)
- * -# combines the generated molecule lists from all subgraphs
- * -# saves to disk: fragment configs, adjacency, orderatsite, keyset files
- * Note that as we split "this" molecule up into a list of subgraphs, i.e. a MoleculeListClass, we have two sets
- * of vertex indices: Global always means the index in "this" molecule, whereas local refers to the molecule or
- * subgraph in the MoleculeListClass.
+ *
+ * \note during fragmentation we switch to so-called local ids, atomic ids
+ * that are valid only for the specific molecule (representing a connected
+ * subgraph of the molecular system).
+ *
+ * -# create the local id to global id mapping
+ * -# parse the adjacency file and require the above mapping for translation
+ * -# initialize a mask for the molecule's atoms, telling which atoms are
+ *    treated and which atoms neglected during fragmentation
+ * -# parse and orderatsite file and check whether there's something to do. This
+      allows for iterative calls to fragmentation
+ * -# fragments from the last fragmentation stored to file are converted into
+ *    keysets (sets of atomic indices that describe one fragment)
+ * -# in a loop as long as order at site is not correct yet
+ *   -# prepare a stack containing the initial ids where the fragmentation or
+ *      rather the graph algorithms start from
+ *   -# call fragmentBOSSANOVA()
+ * -# afterwards in case we don't saturate we remove single-atom fragments
+ * -# translate the local ids of the keysets into global ids.
+ * -# updated order at site file is written
+ *
+ * note that all created fragments or rather their describing key sets are
+ * contained in the Graph Fragmentation::FragmentList.
+ *
  * \param atomids atomic ids (local to Fragmentation::mol) to fragment, used in AtomMask
  * \param Order up to how many neighbouring bonds a fragment contains in BondOrderScheme::BottumUp scheme
  * \param prefix prefix string for every fragment file name (may include path)
+ * \param ParsedFragmentList all already created key sets
  * \return 1 - continue, 2 - stop (no fragmentation occured)
  */