Changeset 6bd7e0 for src/Analysis

Timestamp:

Jan 2, 2012, 1:34:28 PM (13 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:

d78531

Parents:

f55ae5

git-author:

Frederik Heber <heber@…> (12/19/11 16:46:11)

git-committer:

Frederik Heber <heber@…> (01/02/12 13:34:28)

Message:

Renamed old LinkedCell class to LinkedCell_deprecated.

• this is preparatory for a smooth transition to the new implementation.
• note that class LinkedCell and namespace LinkedCell bite each other so far.

Location:

src/Analysis

Files:

• analysis_correlation.cpp (modified) (2 diffs)
• analysis_correlation.hpp (modified) (2 diffs)
• unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) (1 diff)
• unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) (2 diffs)

src/Analysis/analysis_correlation.cpp

@@ -531 +531 @@
  * \param &elements vector of elements to correlate to surface
  * \param *Surface pointer to Tesselation class surface
- * \param *LC LinkedCell structure to quickly find neighbouring atoms
+ * \param *LC LinkedCell_deprecated structure to quickly find neighbouring atoms
  * \return Map of doubles with values as pairs of atom and the BoundaryTriangleSet that's closest
  */
-CorrelationToSurfaceMap *CorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell *LC )
+CorrelationToSurfaceMap *CorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell_deprecated *LC )
 {
   Info FunctionInfo(__func__);
@@ -584 +584 @@
  * \param &elements vector of elements to correlate to surface
  * \param *Surface pointer to Tesselation class surface
- * \param *LC LinkedCell structure to quickly find neighbouring atoms
+ * \param *LC LinkedCell_deprecated structure to quickly find neighbouring atoms
  * \param ranges[NDIM] interval boundaries for the periodic images to scan also
  * \return Map of doubles with values as pairs of atom and the BoundaryTriangleSet that's closest
  */
-CorrelationToSurfaceMap *PeriodicCorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell *LC, const int ranges[NDIM] )
+CorrelationToSurfaceMap *PeriodicCorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell_deprecated *LC, const int ranges[NDIM] )
 {
   Info FunctionInfo(__func__);

src/Analysis/analysis_correlation.hpp

@@ -40 +40 @@
 class Formula;
 class element;
-class LinkedCell;
+class LinkedCell_deprecated;
 class Tesselation;
 class Vector;
@@ -67 +67 @@
 PairCorrelationMap *PairCorrelation(std::vector<molecule *> &molecules, const std::vector<const element *> &elements);
 CorrelationToPointMap *CorrelationToPoint(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Vector *point );
-CorrelationToSurfaceMap *CorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell *LC );
+CorrelationToSurfaceMap *CorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell_deprecated *LC );
 PairCorrelationMap *PeriodicPairCorrelation(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const int ranges[NDIM] );
 CorrelationToPointMap *PeriodicCorrelationToPoint(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Vector *point, const int ranges[NDIM] );
-CorrelationToSurfaceMap *PeriodicCorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell *LC, const int ranges[NDIM] );
+CorrelationToSurfaceMap *PeriodicCorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell_deprecated *LC, const int ranges[NDIM] );
 int GetBin ( const double value, const double BinWidth, const double BinStart );
 void OutputCorrelation_Header( ofstream * const file );

src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp

@@ -102 +102 @@
   Surface = new Tesselation;
   PointCloudAdaptor<molecule> cloud(TestSurfaceMolecule, TestSurfaceMolecule->name);
-  LC = new LinkedCell(cloud, 5.);
-  FindNonConvexBorder(TestSurfaceMolecule, Surface, (const LinkedCell *&)LC, 2.5, NULL);
+  LC = new LinkedCell_deprecated(cloud, 5.);
+  FindNonConvexBorder(TestSurfaceMolecule, Surface, (const LinkedCell_deprecated *&)LC, 2.5, NULL);
 
   // add outer atoms

src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp

@@ -18 +18 @@
 
 class element;
-class LinkedCell;
+class LinkedCell_deprecated;
 class molecule;
 class MoleculeListClass;
@@ -58 +58 @@
       BinPairMap *binmap;
       Tesselation *Surface;
-      LinkedCell *LC;
+      LinkedCell_deprecated *LC;
 };