Changeset 5034e1 for src/atom.cpp

Timestamp:

Oct 12, 2009, 12:10:43 PM (16 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, Candidate_v1.7.0, 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:

d2943b

Parents:

4a7776a

git-author:

Frederik Heber <heber@…> (10/12/09 12:04:44)

git-committer:

Frederik Heber <heber@…> (10/12/09 12:10:43)

Message:

First half of molecule_fragmentation.cpp refactoring.

• new template helper function: IncrementalAbsoluteValue() which also increments itself (fixed by one)
• new template molecule function: SetAtomValueToIndexedArray() which sets an attribute of atom class according to some array
• Store/ParseKeySetFile() removed from class molecule, as there was no need
• molecule::StoreFragmentFromKeySet() split up into: StoreFragmentFromKeySet_Init() and CreateInducedSubgraphOfFragment()
• molecule::CreateMappingLabelsToConfigSequence() uses SetIndexedArrayForEachAtomTo() with new IncrementalAbsoluteValue()
• molecule::ParseOrderAtSiteFromFile() uses SetAtomValueToIndexedArray() on MaxOrder and Adaptive Order
• atom has new member function: OutputOrder()
• molecule::StoreOrderAtSiteFile() uses ActOnAllAtoms with above
• molecule::CheckOrderAtSite() rewritten, new helper functions are: GraphToIndexedKeySet(), ScanAdaptiveFileIntoMap() (therein InsertIntoAdaptiveCriteriaList()), ReMapAdaptiveCriteriaListToValue(), MarkUpdateCandidates(), PrintAtomMask()
• StoreKeySetFile split up, TEFactors are now stored in StoreTEFactorsFile, same goes with Parse...()

File:

• src/atom.cpp (modified) (1 diff)

src/atom.cpp

@@ -339 +339 @@
 };
 
+/** Outputs the current atom::AdaptiveOrder and atom::MaxOrder to \a *file.
+ * \param *file output stream
+ */
+void atom::OutputOrder(ofstream *file)
+{
+  *file << nr << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << endl;
+  //cout << Verbose(2) << "Storing: " << Walker->nr << "\t" << (int)Walker->AdaptiveOrder << "\t" << (int)Walker->MaxOrder << "." << endl;
+}
+
 /** Returns squared distance to a given vector.
  * \param origin vector to calculate distance to