Changeset e6f8b7
- Timestamp:
- May 2, 2008, 1:35:10 PM (17 years ago)
- 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:
- 3b15bb
- Parents:
- db942e
- File:
-
- 1 edited
Legend:
- Unmodified
- Added
- Removed
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TabularUnified src/molecules.cpp ¶
rdb942e re6f8b7 2046 2046 2047 2047 /** Performs a many-body bond order analysis for a given bond order. 2048 * Writes for each fragment a config file. 2048 * -# parses adjacency, keysets and orderatsite files 2049 * -# performs DFS to find connected subgraphs (to leave this in was a design decision: might be useful later) 2050 * -# RootStack is created for every subgraph (here, later we implement the "update 10 sites with highest energ 2051 y contribution", and that's why this consciously not done in the following loop) 2052 * -# in a loop over all subgraphs 2053 * -# calls FragmentBOSSANOVA with this RootStack and within the subgraph molecule structure 2054 * -# creates molecule (fragment)s from the returned keysets (StoreFragmentFromKeySet) 2055 * -# combines the generated molecule lists from all subgraphs 2056 * -# saves to disk: fragment configs, adjacency, orderatsite, keyset files 2049 2057 * \param *out output stream for debugging 2050 2058 * \param Order up to how many neighbouring bonds a fragment contains in BondOrderScheme::BottumUp scheme … … 2937 2945 2938 2946 /** From a given set of Bond sorted by Shortest Path distance, create all possible fragments of size \a SetDimension. 2939 * This basically involves recursion to create all power set combinations. 2947 * -# loops over every possible combination (2^dimension of edge set) 2948 * -# inserts current set, if there's still space left 2949 * -# yes: calls SPFragmentGenerator with structure, created new edge list and size respective to root dist 2950 ance+1 2951 * -# no: stores fragment into keyset list by calling InsertFragmentIntoGraph 2952 * -# removes all items added into the snake stack (in UniqueFragments structure) added during level (root 2953 distance) and current set 2940 2954 * \param *out output stream for debugging 2941 2955 * \param FragmentSearch UniqueFragments structure with all values needed … … 3061 3075 3062 3076 /** Creates a list of all unique fragments of certain vertex size from a given graph \a Fragment for a given root vertex in the context of \a this molecule. 3077 * -# initialises UniqueFragments structure 3078 * -# fills edge list via BFS 3079 * -# creates the fragment by calling recursive function SPFragmentGenerator with UniqueFragments structure, 0 as 3080 root distance, the edge set, its dimension and the current suborder 3081 * -# Free'ing structure 3063 3082 * Note that we may use the fact that the atoms are SP-ordered on the atomstack. I.e. when popping always the last, we first get all 3064 3083 * with SP of 2, then those with SP of 3, then those with SP of 4 and so on. … … 3483 3502 3484 3503 /** Performs BOSSANOVA decomposition at selected sites, increasing the cutoff by one at these sites. 3504 * -# constructs a complete keyset of the molecule 3505 * -# In a loop over all possible roots from the given rootstack 3506 * -# increases order of root site 3507 * -# calls PowerSetGenerator with this order, the complete keyset and the rootkeynr 3508 * -# for all consecutive lower levels PowerSetGenerator is called with the suborder, the higher order keyset 3509 as the restricted one and each site in the set as the root) 3510 * -# these are merged into a fragment list of keysets 3511 * -# All fragment lists (for all orders, i.e. from all destination fields) are merged into one list for return 3485 3512 * Important only is that we create all fragments, it is not important if we create them more than once 3486 3513 * as these copies are filtered out via use of the hash table (KeySet).
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