Changeset 5034e1 for src/molecule.hpp

Timestamp:

Oct 12, 2009, 12:10:43 PM (15 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:

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/molecule.hpp (modified) (2 diffs)

src/molecule.hpp

@@ -177 +177 @@
   // templates for allowing global manipulation of an array with one entry per atom
   void SetIndexedArrayForEachAtomTo ( atom **array, int TesselPoint::* index);
-  template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int TesselPoint::* index, void (*Setor)(T *, T));
-  template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int TesselPoint::* index, void (*Setor)(T *, T), T t);
-  template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::*index, void (*Setor)(T *, T));
-  template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::*index, void (*Setor)(T *, T), T t);
+  template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int TesselPoint::* index, void (*Setor)(T *, T *));
+  template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int TesselPoint::* index, void (*Setor)(T *, T *), T t);
+  template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int TesselPoint::* index, void (*Setor)(T *, T *), T *t);
+  template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::*index, void (*Setor)(T *, T *));
+  template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::*index, void (*Setor)(T *, T *), T t);
+  template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::*index, void (*Setor)(T *, T *), T *t);
   template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int TesselPoint::* index, T (atom::*Setor)(Vector &), Vector atom::*value);
   template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int TesselPoint::*index, T (atom::*Setor)(Vector &), Vector &vect );
+
+  // templates for allowing global manipulation of each atom by entries in an array
+  template <typename T> void SetAtomValueToIndexedArray ( T *array, int TesselPoint::*index, T atom::*value );
+  template <typename T> void SetAtomValueToIndexedArray ( T *array, int element::*index, T atom::*value );
 
   /// remove atoms from molecule.
@@ -267 +273 @@
   bool ParseOrderAtSiteFromFile(ofstream *out, char *path);
   bool StoreOrderAtSiteFile(ofstream *out, char *path);
-  bool ParseKeySetFile(ofstream *out, char *filename, Graph *&FragmentList);
-  bool StoreKeySetFile(ofstream *out, Graph &KeySetList, char *path);
   bool StoreForcesFile(ofstream *out, MoleculeListClass *BondFragments, char *path, int *SortIndex);
   bool CreateMappingLabelsToConfigSequence(ofstream *out, int *&SortIndex);
-  bool ScanBufferIntoKeySet(ofstream *out, char *buffer, KeySet &CurrentSet);
   void BreadthFirstSearchAdd(ofstream *out, molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
   /// -# BOSSANOVA