Changeset 6bd7e0 for src


Ignore:
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
Files:
31 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/AnalysisAction/MolecularVolumeAction.cpp

    rf55ae5 r6bd7e0  
    5050    molecule *mol = iter->second;
    5151    class Tesselation *TesselStruct = NULL;
    52     const LinkedCell *LCList = NULL;
     52    const LinkedCell_deprecated *LCList = NULL;
    5353    LOG(0, "Evaluating volume of the convex envelope.");
    5454    PointCloudAdaptor< molecule > cloud(mol, mol->name);
    55     LCList = new LinkedCell(cloud, 10.);
     55    LCList = new LinkedCell_deprecated(cloud, 10.);
    5656    config * const configuration = World::getInstance().getConfig();
    5757    //Boundaries *BoundaryPoints = NULL;

  • src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

    rf55ae5 r6bd7e0  
    7171  // get the boundary
    7272  class Tesselation *TesselStruct = NULL;
    73   const LinkedCell *LCList = NULL;
     73  const LinkedCell_deprecated *LCList = NULL;
    7474  // find biggest molecule
    7575  std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
    7676  std::cout << "There are " << molecules.size() << " selected molecules." << std::endl;
    7777  PointCloudAdaptor<molecule> cloud(surfacemol, surfacemol->name);
    78   LCList = new LinkedCell(cloud, LCWidth);
     78  LCList = new LinkedCell_deprecated(cloud, LCWidth);
    7979  FindNonConvexBorder(surfacemol, TesselStruct, LCList, radius, NULL);
    8080  CorrelationToSurfaceMap *surfacemap = NULL;

  • src/Actions/TesselationAction/ConvexEnvelopeAction.cpp

    rf55ae5 r6bd7e0  
    5151    mol = iter->second;
    5252    class Tesselation *TesselStruct = NULL;
    53     const LinkedCell *LCList = NULL;
     53    const LinkedCell_deprecated *LCList = NULL;
    5454    LOG(0, "Evaluating volume of the convex envelope.");
    5555    LOG(1, "Storing tecplot convex data in " << params.filenameConvex << ".");
    5656    LOG(1, "Storing tecplot non-convex data in " << params.filenameNonConvex << ".");
    5757    PointCloudAdaptor<molecule> cloud(mol, mol->name);
    58     LCList = new LinkedCell(cloud, 100.);
     58    LCList = new LinkedCell_deprecated(cloud, 100.);
    5959    //Boundaries *BoundaryPoints = NULL;
    6060    //FindConvexBorder(mol, BoundaryPoints, TesselStruct, LCList, argv[argptr]);

  • src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp

    rf55ae5 r6bd7e0  
    5050    Boundary = iter->second;
    5151    class Tesselation *T = NULL;
    52     const LinkedCell *LCList = NULL;
     52    const LinkedCell_deprecated *LCList = NULL;
    5353    LOG(0, "Evaluating non-convex envelope of molecule." << Boundary->getId());
    5454    LOG(1, "Using rolling ball of radius " << params.SphereRadius << " and storing tecplot data in " << params.filename << ".");
    … …  
    5656    start = clock();
    5757    PointCloudAdaptor< molecule > cloud(Boundary, Boundary->name);
    58     LCList = new LinkedCell(cloud, params.SphereRadius*2.);
     58    LCList = new LinkedCell_deprecated(cloud, params.SphereRadius*2.);
    5959    Success = FindNonConvexBorder(Boundary, T, LCList, params.SphereRadius, params.filename.string().c_str());
    6060    //FindDistributionOfEllipsoids(T, &LCList, N, number, params.filename.c_str());

  • src/Analysis/analysis_correlation.cpp

    rf55ae5 r6bd7e0  
    531531 * \param &elements vector of elements to correlate to surface
    532532 * \param *Surface pointer to Tesselation class surface
    533  * \param *LC LinkedCell structure to quickly find neighbouring atoms
     533 * \param *LC LinkedCell_deprecated structure to quickly find neighbouring atoms
    534534 * \return Map of doubles with values as pairs of atom and the BoundaryTriangleSet that's closest
    535535 */
    536 CorrelationToSurfaceMap *CorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell *LC )
     536CorrelationToSurfaceMap *CorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell_deprecated *LC )
    537537{
    538538  Info FunctionInfo(__func__);
    … …  
    584584 * \param &elements vector of elements to correlate to surface
    585585 * \param *Surface pointer to Tesselation class surface
    586  * \param *LC LinkedCell structure to quickly find neighbouring atoms
     586 * \param *LC LinkedCell_deprecated structure to quickly find neighbouring atoms
    587587 * \param ranges[NDIM] interval boundaries for the periodic images to scan also
    588588 * \return Map of doubles with values as pairs of atom and the BoundaryTriangleSet that's closest
    589589 */
    590 CorrelationToSurfaceMap *PeriodicCorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell *LC, const int ranges[NDIM] )
     590CorrelationToSurfaceMap *PeriodicCorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell_deprecated *LC, const int ranges[NDIM] )
    591591{
    592592  Info FunctionInfo(__func__);

  • src/Analysis/analysis_correlation.hpp

    rf55ae5 r6bd7e0  
    4040class Formula;
    4141class element;
    42 class LinkedCell;
     42class LinkedCell_deprecated;
    4343class Tesselation;
    4444class Vector;
    … …  
    6767PairCorrelationMap *PairCorrelation(std::vector<molecule *> &molecules, const std::vector<const element *> &elements);
    6868CorrelationToPointMap *CorrelationToPoint(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Vector *point );
    69 CorrelationToSurfaceMap *CorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell *LC );
     69CorrelationToSurfaceMap *CorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell_deprecated *LC );
    7070PairCorrelationMap *PeriodicPairCorrelation(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const int ranges[NDIM] );
    7171CorrelationToPointMap *PeriodicCorrelationToPoint(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Vector *point, const int ranges[NDIM] );
    72 CorrelationToSurfaceMap *PeriodicCorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell *LC, const int ranges[NDIM] );
     72CorrelationToSurfaceMap *PeriodicCorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell_deprecated *LC, const int ranges[NDIM] );
    7373int GetBin ( const double value, const double BinWidth, const double BinStart );
    7474void OutputCorrelation_Header( ofstream * const file );

  • src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp

    rf55ae5 r6bd7e0  
    102102  Surface = new Tesselation;
    103103  PointCloudAdaptor<molecule> cloud(TestSurfaceMolecule, TestSurfaceMolecule->name);
    104   LC = new LinkedCell(cloud, 5.);
    105   FindNonConvexBorder(TestSurfaceMolecule, Surface, (const LinkedCell *&)LC, 2.5, NULL);
     104  LC = new LinkedCell_deprecated(cloud, 5.);
     105  FindNonConvexBorder(TestSurfaceMolecule, Surface, (const LinkedCell_deprecated *&)LC, 2.5, NULL);
    106106
    107107  // add outer atoms

  • src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp

    rf55ae5 r6bd7e0  
    1818
    1919class element;
    20 class LinkedCell;
     20class LinkedCell_deprecated;
    2121class molecule;
    2222class MoleculeListClass;
    … …  
    5858      BinPairMap *binmap;
    5959      Tesselation *Surface;
    60       LinkedCell *LC;
     60      LinkedCell_deprecated *LC;
    6161};
    6262

  • src/Graph/BondGraph.cpp

    rf55ae5 r6bd7e0  
    169169}
    170170
    171 void BondGraph::CreateAdjacency(LinkedCell &LC) const
     171void BondGraph::CreateAdjacency(LinkedCell_deprecated &LC) const
    172172{
    173173  atom *Walker = NULL;

  • src/Graph/BondGraph.hpp

    rf55ae5 r6bd7e0  
    7676   *
    7777   * I.e. the function returns a sensible cutoff criteria for bond recognition,
    78    * e.g. to be used for LinkedCell or others.
     78   * e.g. to be used for LinkedCell_deprecated or others.
    7979   *
    8080   * \param &Set AtomSetMixin with all particles to consider
    … …  
    149149      LOG(1, "STATUS: Creating LinkedCell structure for given " << counter << " atoms.");
    150150      PointCloudAdaptor< AtomSetMixin<container_type,iterator_type> > cloud(&Set, "SetOfAtoms");
    151       LinkedCell *LC = new LinkedCell(cloud, max_distance);
     151      LinkedCell_deprecated *LC = new LinkedCell_deprecated(cloud, max_distance);
    152152
    153153      CreateAdjacency(*LC);
    … …  
    258258   * \param &LC Linked Cell Container with all atoms
    259259   */
    260   void CreateAdjacency(LinkedCell &LC) const;
     260  void CreateAdjacency(LinkedCell_deprecated &LC) const;
    261261
    262262  /** Removes all bonds within the given set of iterable atoms.

  • src/LinkedCell/linkedcell.cpp

    rf55ae5 r6bd7e0  
    88/** \file linkedcell.cpp
    99 *
    10  * Function implementations for the class LinkedCell.
     10 * Function implementations for the class LinkedCell_deprecated.
    1111 *
    1212 */
    … …  
    3030#include "Tesselation/tesselation.hpp"
    3131
    32 // ========================================================= class LinkedCell ===========================================
    33 
    34 /** Constructor for class LinkedCell.
    35  */
    36 LinkedCell::LinkedCell() :
     32// ========================================================= class LinkedCell_deprecated ===========================================
     33
     34/** Constructor for class LinkedCell_deprecated.
     35 */
     36LinkedCell_deprecated::LinkedCell_deprecated() :
    3737  LC(NULL),
    3838  RADIUS(0.),
    … …  
    4949 * \param RADIUS edge length of cells
    5050 */
    51 LinkedCell::LinkedCell(IPointCloud & set, const double radius) :
     51LinkedCell_deprecated::LinkedCell_deprecated(IPointCloud & set, const double radius) :
    5252  LC(NULL),
    5353  RADIUS(radius),
    … …  
    122122
    123123
    124 /** Destructor for class LinkedCell.
    125  */
    126 LinkedCell::~LinkedCell()
     124/** Destructor for class LinkedCell_deprecated.
     125 */
     126LinkedCell_deprecated::~LinkedCell_deprecated()
    127127{
    128128  if (LC != NULL)
    … …  
    135135};
    136136
    137 /** Checks whether LinkedCell::n[] is each within [0,N[]].
     137/** Checks whether LinkedCell_deprecated::n[] is each within [0,N[]].
    138138 * \return if all in intervals - true, else -false
    139139 */
    140 bool LinkedCell::CheckBounds() const
     140bool LinkedCell_deprecated::CheckBounds() const
    141141{
    142142  bool status = true;
    … …  
    148148};
    149149
    150 /** Checks whether LinkedCell::n[] plus relative offset is each within [0,N[]].
     150/** Checks whether LinkedCell_deprecated::n[] plus relative offset is each within [0,N[]].
    151151 * Note that for this check we don't admonish if out of bounds.
    152152 * \param relative[NDIM] relative offset to current cell
    153153 * \return if all in intervals - true, else -false
    154154 */
    155 bool LinkedCell::CheckBounds(const int relative[NDIM]) const
     155bool LinkedCell_deprecated::CheckBounds(const int relative[NDIM]) const
    156156{
    157157  bool status = true;
    … …  
    163163
    164164/** Returns a pointer to the current cell.
    165  * \return LinkedAtoms pointer to current cell, NULL if LinkedCell::n[] are out of bounds.
    166  */
    167 const TesselPointSTLList* LinkedCell::GetCurrentCell() const
     165 * \return LinkedAtoms pointer to current cell, NULL if LinkedCell_deprecated::n[] are out of bounds.
     166 */
     167const TesselPointSTLList* LinkedCell_deprecated::GetCurrentCell() const
    168168{
    169169  if (CheckBounds()) {
    … …  
    176176
    177177/** Returns a pointer to the current cell.
    178  * \param relative[NDIM] offset for each axis with respect to the current cell LinkedCell::n[NDIM]
    179  * \return LinkedAtoms pointer to current cell, NULL if LinkedCell::n[]+relative[] are out of bounds.
    180  */
    181 const TesselPointSTLList* LinkedCell::GetRelativeToCurrentCell(const int relative[NDIM]) const
     178 * \param relative[NDIM] offset for each axis with respect to the current cell LinkedCell_deprecated::n[NDIM]
     179 * \return LinkedAtoms pointer to current cell, NULL if LinkedCell_deprecated::n[]+relative[] are out of bounds.
     180 */
     181const TesselPointSTLList* LinkedCell_deprecated::GetRelativeToCurrentCell(const int relative[NDIM]) const
    182182{
    183183  if (CheckBounds(relative)) {
    … …  
    193193 * \return Vector is inside bounding box - true, else - false
    194194 */
    195 bool LinkedCell::SetIndexToVector(const Vector & x) const
     195bool LinkedCell_deprecated::SetIndexToVector(const Vector & x) const
    196196{
    197197  for (int i=0;i<NDIM;i++)
    … …  
    205205 * \return if the atom is also found in this cell - true, else - false
    206206 */
    207 bool LinkedCell::SetIndexToNode(const TesselPoint * const Walker) const
     207bool LinkedCell_deprecated::SetIndexToNode(const TesselPoint * const Walker) const
    208208{
    209209  bool status = false;
    … …  
    227227 * \param step how deep to check the neighbouring cells (i.e. number of layers to check)
    228228 */
    229 void LinkedCell::GetNeighbourBounds(int lower[NDIM], int upper[NDIM], int step) const
     229void LinkedCell_deprecated::GetNeighbourBounds(int lower[NDIM], int upper[NDIM], int step) const
    230230{
    231231  for (int i=0;i<NDIM;i++) {
    … …  
    244244};
    245245
    246 /** Returns a list with all neighbours from the current LinkedCell::index.
     246/** Returns a list with all neighbours from the current LinkedCell_deprecated::index.
    247247 * \param distance (if no distance, then adjacent cells are taken)
    248248 * \return list of tesselpoints
    249249 */
    250 TesselPointSTLList* LinkedCell::GetallNeighbours(const double distance) const
     250TesselPointSTLList* LinkedCell_deprecated::GetallNeighbours(const double distance) const
    251251{
    252252  int Nlower[NDIM], Nupper[NDIM];
    … …  
    273273};
    274274
    275 /** Set the index to the cell containing a given Vector *x, which is not inside the LinkedCell's domain
     275/** Set the index to the cell containing a given Vector *x, which is not inside the LinkedCell_deprecated's domain
    276276 * Note that as we have to check distance from every corner of the closest cell, this function is faw more
    277  * expensive and if Vector is known to be inside LinkedCell's domain, then SetIndexToVector() should be used.
     277 * expensive and if Vector is known to be inside LinkedCell_deprecated's domain, then SetIndexToVector() should be used.
    278278 * \param *x Vector with coordinates
    279279 * \return minimum squared distance of cell to given vector (if inside of domain, distance is 0)
    280280 */
    281 double LinkedCell::SetClosestIndexToOutsideVector(const Vector * const x) const
     281double LinkedCell_deprecated::SetClosestIndexToOutsideVector(const Vector * const x) const
    282282{
    283283  for (int i=0;i<NDIM;i++) {
    … …  
    291291  // calculate distance of cell to vector
    292292  double distanceSquared = 0.;
    293   bool outside = true;  // flag whether x is found in- or outside of LinkedCell's domain/closest cell
     293  bool outside = true;  // flag whether x is found in- or outside of LinkedCell_deprecated's domain/closest cell
    294294  Vector corner; // current corner of closest cell
    295295  Vector tester; // Vector pointing from corner to center of closest cell
    … …  
    326326 * \return list of all points inside sphere
    327327 */
    328 TesselPointSTLList* LinkedCell::GetPointsInsideSphere(const double radius, const Vector * const center) const
     328TesselPointSTLList* LinkedCell_deprecated::GetPointsInsideSphere(const double radius, const Vector * const center) const
    329329{
    330330  const double radiusSquared = radius*radius;

  • src/LinkedCell/linkedcell.hpp

    rf55ae5 r6bd7e0  
    4848/** Linked Cell class for containing Vectors in real space efficiently.
    4949 */
    50 class LinkedCell {
     50class LinkedCell_deprecated {
    5151private:
    5252
    … …  
    6060    mutable int index;        // temporary index variable , access by index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
    6161
    62     LinkedCell();
    63     LinkedCell(IPointCloud &set, const double radius);
    64     ~LinkedCell();
     62    LinkedCell_deprecated();
     63    LinkedCell_deprecated(IPointCloud &set, const double radius);
     64    ~LinkedCell_deprecated();
    6565    const TesselPointSTLList* GetCurrentCell()const ;
    6666    const TesselPointSTLList* GetRelativeToCurrentCell(const int relative[NDIM])const ;

  • src/LinkedCell/unittests/linkedcellUnitTest.cpp

    rf55ae5 r6bd7e0  
    7676  // construct linked cell
    7777  PointCloudAdaptor<molecule> cloud(TestMolecule, TestMolecule->name);
    78   LC = new LinkedCell (cloud, 1.);
     78  LC = new LinkedCell_deprecated (cloud, 1.);
    7979  CPPUNIT_ASSERT(LC != NULL && "could not create LinkedCell");
    8080
    … …  
    9191
    9292
    93 /** UnitTest for LinkedCell::CheckBounds().
     93/** UnitTest for LinkedCell_deprecated::CheckBounds().
    9494 */
    9595void linkedcelltest::CheckBoundsTest()
    … …  
    121121
    122122
    123 /** UnitTest for LinkedCell::GetCurrentCell().
     123/** UnitTest for LinkedCell_deprecated::GetCurrentCell().
    124124 * Note that CheckBounds() is used and has to be tested already.
    125125 */
    … …  
    143143};
    144144
    145 /** UnitTest for LinkedCell::GetRelativeToCurrentCell().
     145/** UnitTest for LinkedCell_deprecated::GetRelativeToCurrentCell().
    146146 */
    147147void linkedcelltest::GetRelativeToCurrentCellTest()
    … …  
    200200
    201201
    202 /** UnitTest for LinkedCell::SetIndexToNode().
     202/** UnitTest for LinkedCell_deprecated::SetIndexToNode().
    203203 */
    204204void linkedcelltest::SetIndexToNodeTest()
    … …  
    225225
    226226
    227 /** UnitTest for LinkedCell::SetIndexToVector().
     227/** UnitTest for LinkedCell_deprecated::SetIndexToVector().
    228228 */
    229229void linkedcelltest::SetIndexToVectorTest()
    … …  
    261261
    262262
    263 /** UnitTest for LinkedCell::GetNeighbourBounds().
     263/** UnitTest for LinkedCell_deprecated::GetNeighbourBounds().
    264264 */
    265265void linkedcelltest::GetNeighbourBoundsTest()
    … …  
    278278
    279279
    280 /** UnitTest for LinkedCell::GetallNeighbours().
     280/** UnitTest for LinkedCell_deprecated::GetallNeighbours().
    281281 */
    282282void linkedcelltest::GetallNeighboursTest()
    … …  
    339339
    340340
    341 /** UnitTest for LinkedCell::GetPointsInsideSphere().
     341/** UnitTest for LinkedCell_deprecated::GetPointsInsideSphere().
    342342 */
    343343void linkedcelltest::GetPointsInsideSphereTest()

  • src/LinkedCell/unittests/linkedcellUnitTest.hpp

    rf55ae5 r6bd7e0  
    1919
    2020class element;
    21 class LinkedCell;
     21class LinkedCell_deprecated;
    2222class molecule;
    2323class periodentafel;
    … …  
    5555      molecule *TestMolecule;
    5656      const element *hydrogen;
    57       LinkedCell *LC;
     57      LinkedCell_deprecated *LC;
    5858};
    5959

  • src/Tesselation/CandidateForTesselation.cpp

    rf55ae5 r6bd7e0  
    7979 * Sphere must touch all candidates and the baseline endpoints and there must be no other atoms inside.
    8080 * \param RADIUS radius of sphere
    81  * \param *LC LinkedCell structure with other atoms
     81 * \param *LC LinkedCell_deprecated structure with other atoms
    8282 * \return true - sphere is valid, false - sphere contains other points
    8383 */
    84 bool CandidateForTesselation::CheckValidity(const double RADIUS, const LinkedCell *LC) const
     84bool CandidateForTesselation::CheckValidity(const double RADIUS, const LinkedCell_deprecated *LC) const
    8585{
    8686  Info FunctionInfo(__func__);

  • src/Tesselation/CandidateForTesselation.hpp

    rf55ae5 r6bd7e0  
    2424class BoundaryPointSet;
    2525class BoundaryTriangleSet;
    26 class LinkedCell;
     26class LinkedCell_deprecated;
    2727class TesselPoint;
    2828
    … …  
    3333  ~CandidateForTesselation();
    3434
    35   bool CheckValidity(const double RADIUS, const class LinkedCell *LC) const;
     35  bool CheckValidity(const double RADIUS, const class LinkedCell_deprecated *LC) const;
    3636
    3737  TesselPointList pointlist;

  • src/Tesselation/boundary.cpp

    rf55ae5 r6bd7e0  
    322322 * \param *BoundaryPts set of boundary points to use or NULL
    323323 * \param *TesselStruct Tesselation filled with points, lines and triangles on boundary on return
    324  * \param *LCList atoms in LinkedCell list
     324 * \param *LCList atoms in LinkedCell_deprecated list
    325325 * \param *filename filename prefix for output of vertex data
    326326 * \return *TesselStruct is filled with convex boundary and tesselation is stored under \a *filename.
    327327 */
    328 void FindConvexBorder(const molecule* mol, Boundaries *BoundaryPts, Tesselation *&TesselStruct, const LinkedCell *LCList, const char *filename)
     328void FindConvexBorder(const molecule* mol, Boundaries *BoundaryPts, Tesselation *&TesselStruct, const LinkedCell_deprecated *LCList, const char *filename)
    329329{
    330330        Info FunctionInfo(__func__);
    … …  
    711711  GreatestDiameter = GetDiametersOfCluster(BoundaryPoints, mol, TesselStruct, IsAngstroem);
    712712  PointCloudAdaptor< molecule > cloud(mol, mol->name);
    713   LinkedCell *LCList = new LinkedCell(cloud, 10.);
    714   FindConvexBorder(mol, BoundaryPoints, TesselStruct, (const LinkedCell *&)LCList, NULL);
     713  LinkedCell_deprecated *LCList = new LinkedCell_deprecated(cloud, 10.);
     714  FindConvexBorder(mol, BoundaryPoints, TesselStruct, (const LinkedCell_deprecated *&)LCList, NULL);
    715715  delete (LCList);
    716716  delete[] BoundaryPoints;
    … …  
    815815  double phi[NDIM];
    816816  map<molecule *, Tesselation *> TesselStruct;
    817   map<molecule *, LinkedCell *> LCList;
     817  map<molecule *, LinkedCell_deprecated *> LCList;
    818818
    819819  for (MoleculeList::iterator ListRunner = List->ListOfMolecules.begin(); ListRunner != List->ListOfMolecules.end(); ListRunner++)
    … …  
    821821      LOG(1, "Pre-creating linked cell lists for molecule " << *ListRunner << ".");
    822822      PointCloudAdaptor< molecule > cloud(*ListRunner, (*ListRunner)->name);
    823       LCList[(*ListRunner)] = new LinkedCell(cloud, 10.); // get linked cell list
     823      LCList[(*ListRunner)] = new LinkedCell_deprecated(cloud, 10.); // get linked cell list
    824824      LOG(1, "Pre-creating tesselation for molecule " << *ListRunner << ".");
    825825      TesselStruct[(*ListRunner)] = NULL;
    826       FindNonConvexBorder((*ListRunner), TesselStruct[(*ListRunner)], (const LinkedCell *&)LCList[(*ListRunner)], 5., NULL);
     826      FindNonConvexBorder((*ListRunner), TesselStruct[(*ListRunner)], (const LinkedCell_deprecated *&)LCList[(*ListRunner)], 5., NULL);
    827827    }
    828828
    … …  
    10171017/** Checks whether there are no atoms inside a sphere around \a CurrentPosition
    10181018 *  except those atoms present in \a *filler.
    1019  *  If filler is NULL, then we just call LinkedCell::GetPointsInsideSphere() and
     1019 *  If filler is NULL, then we just call LinkedCell_deprecated::GetPointsInsideSphere() and
    10201020 *  check whether the return list is empty.
    10211021 * @param *filler
    … …  
    10241024 */
    10251025bool isSpaceAroundPointVoid(
    1026     LinkedCell *LC,
     1026    LinkedCell_deprecated *LC,
    10271027    molecule *filler,
    10281028    const double boundary,
    … …  
    11111111  bool firstInsertion = true;
    11121112  const Box &Domain = World::getInstance().getDomain();
    1113   map<molecule *, LinkedCell *> LCList;
     1113  map<molecule *, LinkedCell_deprecated *> LCList;
    11141114  std::vector<molecule *> List = World::getInstance().getAllMolecules();
    11151115  MoleculeListClass *MolList = World::getInstance().getMolecules();
    … …  
    11191119      LOG(1, "Pre-creating linked cell lists for molecule " << *ListRunner << ".");
    11201120      PointCloudAdaptor< molecule > cloud(*ListRunner, (*ListRunner)->name);
    1121       LCList[(*ListRunner)] = new LinkedCell(cloud, 10.); // get linked cell list
     1121      LCList[(*ListRunner)] = new LinkedCell_deprecated(cloud, 10.); // get linked cell list
    11221122    }
    11231123
    … …  
    11691169        // Check whether there is anything too close by and whether atom is outside of domain
    11701170        FillIt = true;
    1171         for (std::map<molecule *, LinkedCell *>::iterator ListRunner = LCList.begin(); ListRunner != LCList.end(); ++ListRunner) {
     1171        for (std::map<molecule *, LinkedCell_deprecated *>::iterator ListRunner = LCList.begin(); ListRunner != LCList.end(); ++ListRunner) {
    11721172          FillIt = FillIt && isSpaceAroundPointVoid(
    11731173              ListRunner->second,
    … …  
    12341234  LOG(0, MolList->ListOfMolecules.size() << " molecules have been inserted.");
    12351235
    1236   for (std::map<molecule *, LinkedCell *>::iterator ListRunner = LCList.begin(); !LCList.empty(); ListRunner = LCList.begin()) {
     1236  for (std::map<molecule *, LinkedCell_deprecated *>::iterator ListRunner = LCList.begin(); !LCList.empty(); ListRunner = LCList.begin()) {
    12371237    delete ListRunner->second;
    12381238    LCList.erase(ListRunner);
    … …  
    12441244 * \param *mol molecule structure with Atom's and Bond's
    12451245 * \param *&TesselStruct Tesselation filled with points, lines and triangles on boundary on return
    1246  * \param *&LCList atoms in LinkedCell list
     1246 * \param *&LCList atoms in LinkedCell_deprecated list
    12471247 * \param RADIUS radius of the virtual sphere
    12481248 * \param *filename filename prefix for output of vertex data
    12491249 * \return true - tesselation successful, false - tesselation failed
    12501250 */
    1251 bool FindNonConvexBorder(molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LCList, const double RADIUS, const char *filename = NULL)
     1251bool FindNonConvexBorder(molecule* const mol, Tesselation *&TesselStruct, const LinkedCell_deprecated *&LCList, const double RADIUS, const char *filename = NULL)
    12521252{
    12531253        Info FunctionInfo(__func__);
    … …  
    12721272  PointCloudAdaptor< molecule > cloud(mol, mol->name);
    12731273  if (LCList == NULL) {
    1274     LCList = new LinkedCell(cloud, 2.*RADIUS);
     1274    LCList = new LinkedCell_deprecated(cloud, 2.*RADIUS);
    12751275    freeLC = true;
    12761276  }

  • src/Tesselation/boundary.hpp

    rf55ae5 r6bd7e0  
    2424class BoundaryTriangleSet;
    2525class config;
    26 class LinkedCell;
     26class LinkedCell_deprecated;
    2727class molecule;
    2828class MoleculeListClass;
    … …  
    4242void FillBoxWithMolecule(MoleculeListClass *List, molecule *filler, config &configuration, const double MaxDistance, const double distance[NDIM], const double boundary, const double RandomAtomDisplacement, const double RandomMolDisplacement, const bool DoRandomRotation);
    4343void FillVoidWithMolecule(molecule *&filler, config &configuration, const double distance[NDIM], const double boundary, const double RandomAtomDisplacement, const double RandomMolDisplacement, const double MinDistance, const bool DoRandomRotation);
    44 void FindConvexBorder(const molecule* const mol, Boundaries *BoundaryPts, Tesselation *&TesselStruct, const LinkedCell *LCList, const char *filename);
     44void FindConvexBorder(const molecule* const mol, Boundaries *BoundaryPts, Tesselation *&TesselStruct, const LinkedCell_deprecated *LCList, const char *filename);
    4545Vector* FindEmbeddingHole(MoleculeListClass *mols, molecule *srcmol);
    46 bool FindNonConvexBorder(molecule* const mol, Tesselation *&TesselStruct, const LinkedCell *&LC, const double RADIUS, const char *tempbasename);
     46bool FindNonConvexBorder(molecule* const mol, Tesselation *&TesselStruct, const LinkedCell_deprecated *&LC, const double RADIUS, const char *tempbasename);
    4747Boundaries *GetBoundaryPoints(const molecule *mol, Tesselation *&TesselStruct);
    4848double * GetDiametersOfCluster(const Boundaries *BoundaryPtr, const molecule *mol, Tesselation *&TesselStruct, const bool IsAngstroem);

  • src/Tesselation/ellipsoid.cpp

    rf55ae5 r6bd7e0  
    242242 * \param PointsToPick number of points in set to pick
    243243 */
    244 void PickRandomNeighbouredPointSet(class Tesselation *T, class LinkedCell *LC, Vector *&x, size_t PointsToPick)
     244void PickRandomNeighbouredPointSet(class Tesselation *T, class LinkedCell_deprecated *LC, Vector *&x, size_t PointsToPick)
    245245{
    246246  size_t PointsLeft = 0;
    … …  
    414414 * \param *filename name for output file
    415415 */
    416 void FindDistributionOfEllipsoids(class Tesselation *T, class LinkedCell *LCList, int N, int number, const char *filename)
     416void FindDistributionOfEllipsoids(class Tesselation *T, class LinkedCell_deprecated *LCList, int N, int number, const char *filename)
    417417{
    418418  ofstream output;

  • src/Tesselation/ellipsoid.hpp

    rf55ae5 r6bd7e0  
    2222/****************************************** forward declarations *****************************/
    2323
    24 class LinkedCell;
     24class LinkedCell_deprecated;
    2525class Vector;
    2626
    … …  
    3131bool FitPointSetToEllipsoid(Vector *set, int N, Vector *EllipsoidCenter, double *EllipsoidLength, double *EllipsoidAngle);
    3232void PickRandomPointSet(class Tesselation *T, Vector *&x, size_t PointsToPick);
    33 void PickRandomNeighbouredPointSet(class Tesselation *T, class LinkedCell *LC, Vector *&x, size_t PointsToPick);
    34 void FindDistributionOfEllipsoids(class Tesselation *T, class LinkedCell *LCList, int N, int number, const char *filename);
     33void PickRandomNeighbouredPointSet(class Tesselation *T, class LinkedCell_deprecated *LC, Vector *&x, size_t PointsToPick);
     34void FindDistributionOfEllipsoids(class Tesselation *T, class LinkedCell_deprecated *LCList, int N, int number, const char *filename);
    3535
    3636#endif /* ELLIPSOID_HPP_ */

  • src/Tesselation/tesselation.cpp

    rf55ae5 r6bd7e0  
    415415 * \param *out output stream for debugging
    416416 * \param *cloud cluster of points
    417  * \param *LC LinkedCell structure to find nearest point quickly
     417 * \param *LC LinkedCell_deprecated structure to find nearest point quickly
    418418 * \return true - all straddling points insert, false - something went wrong
    419419 */
    420 bool Tesselation::InsertStraddlingPoints(IPointCloud & cloud, const LinkedCell *LC)
     420bool Tesselation::InsertStraddlingPoints(IPointCloud & cloud, const LinkedCell_deprecated *LC)
    421421{
    422422  Info FunctionInfo(__func__);
    … …  
    426426  TriangleList *triangles = NULL;
    427427  bool AddFlag = false;
    428   LinkedCell *BoundaryPoints = NULL;
     428  LinkedCell_deprecated *BoundaryPoints = NULL;
    429429  bool SuccessFlag = true;
    430430
    431431  cloud.GoToFirst();
    432432  PointCloudAdaptor< Tesselation, MapValueIterator<Tesselation::iterator> > newcloud(this, cloud.GetName());
    433   BoundaryPoints = new LinkedCell(newcloud, 5.);
     433  BoundaryPoints = new LinkedCell_deprecated(newcloud, 5.);
    434434  while (!cloud.IsEnd()) { // we only have to go once through all points, as boundary can become only bigger
    435435    if (AddFlag) {
    436436      delete (BoundaryPoints);
    437       BoundaryPoints = new LinkedCell(newcloud, 5.);
     437      BoundaryPoints = new LinkedCell_deprecated(newcloud, 5.);
    438438      AddFlag = false;
    439439    }
    … …  
    846846 * \param &CandidateLine contains other degenerated candidates which we have to subtract as well
    847847 * \param RADIUS radius of sphere
    848  * \param *LC LinkedCell structure with other atoms
     848 * \param *LC LinkedCell_deprecated structure with other atoms
    849849 * \return true - candidate triangle is degenerated, false - candidate triangle is not degenerated
    850850 */
    851 bool Tesselation::CheckDegeneracy(CandidateForTesselation &CandidateLine, const double RADIUS, const LinkedCell *LC) const
     851bool Tesselation::CheckDegeneracy(CandidateForTesselation &CandidateLine, const double RADIUS, const LinkedCell_deprecated *LC) const
    852852{
    853853  Info FunctionInfo(__func__);
    … …  
    997997 * \param *out output stream for debugging
    998998 * \param RADIUS radius of virtual rolling sphere
    999  * \param *LC LinkedCell structure with neighbouring TesselPoint's
     999 * \param *LC LinkedCell_deprecated structure with neighbouring TesselPoint's
    10001000 * \return true - a starting triangle has been created, false - no valid triple of points found
    10011001 */
    1002 bool Tesselation::FindStartingTriangle(const double RADIUS, const LinkedCell *LC)
     1002bool Tesselation::FindStartingTriangle(const double RADIUS, const LinkedCell_deprecated *LC)
    10031003{
    10041004  Info FunctionInfo(__func__);
    … …  
    11301130 * \param *ThirdNode third point in triangle, not in BoundaryLineSet::endpoints
    11311131 * \param RADIUS radius of sphere
    1132  * \param *LC LinkedCell structure
     1132 * \param *LC LinkedCell_deprecated structure
    11331133 * \return true - there is a better candidate (smaller angle than \a ShortestAngle), false - no better TesselPoint candidate found
    11341134 */
    1135 //bool Tesselation::HasOtherBaselineBetterCandidate(CandidateForTesselation &CandidateLine, const TesselPoint * const ThirdNode, double RADIUS, const LinkedCell * const LC) const
     1135//bool Tesselation::HasOtherBaselineBetterCandidate(CandidateForTesselation &CandidateLine, const TesselPoint * const ThirdNode, double RADIUS, const LinkedCell_deprecated * const LC) const
    11361136//{
    11371137//      Info FunctionInfo(__func__);
    … …  
    12701270 * @param RADIUS radius of the rolling ball
    12711271 * @param N number of found triangles
    1272  * @param *LC LinkedCell structure with neighbouring points
    1273  */
    1274 bool Tesselation::FindNextSuitableTriangle(CandidateForTesselation &CandidateLine, const BoundaryTriangleSet &T, const double& RADIUS, const LinkedCell *LC)
     1272 * @param *LC LinkedCell_deprecated structure with neighbouring points
     1273 */
     1274bool Tesselation::FindNextSuitableTriangle(CandidateForTesselation &CandidateLine, const BoundaryTriangleSet &T, const double& RADIUS, const LinkedCell_deprecated *LC)
    12751275{
    12761276  Info FunctionInfo(__func__);
    … …  
    13451345
    13461346/** Walks through Tesselation::OpenLines() and finds candidates for newly created ones.
    1347  * \param *&LCList atoms in LinkedCell list
     1347 * \param *&LCList atoms in LinkedCell_deprecated list
    13481348 * \param RADIUS radius of the virtual sphere
    13491349 * \return true - for all open lines without candidates so far, a candidate has been found,
    13501350 *         false - at least one open line without candidate still
    13511351 */
    1352 bool Tesselation::FindCandidatesforOpenLines(const double RADIUS, const LinkedCell *&LCList)
     1352bool Tesselation::FindCandidatesforOpenLines(const double RADIUS, const LinkedCell_deprecated *&LCList)
    13531353{
    13541354  bool TesselationFailFlag = true;
    … …  
    13721372 * \param CandidateLine triangle to add
    13731373 * \param RADIUS Radius of sphere
    1374  * \param *LC LinkedCell structure
     1374 * \param *LC LinkedCell_deprecated structure
    13751375 * \NOTE we need the copy operator here as the original CandidateForTesselation is removed in
    13761376 * AddTesselationLine() in AddCandidateTriangle()
    13771377 */
    1378 void Tesselation::AddCandidatePolygon(CandidateForTesselation CandidateLine, const double RADIUS, const LinkedCell *LC)
     1378void Tesselation::AddCandidatePolygon(CandidateForTesselation CandidateLine, const double RADIUS, const LinkedCell_deprecated *LC)
    13791379{
    13801380  Info FunctionInfo(__func__);
    … …  
    14681468 * \param CandidateLine CanddiateForTesselation structure for the desired BoundaryLine
    14691469 * \param RADIUS radius of sphere
    1470  * \param *LC pointer to LinkedCell structure
    1471  */
    1472 void Tesselation::AddDegeneratedTriangle(CandidateForTesselation &CandidateLine, const double RADIUS, const LinkedCell *LC)
     1470 * \param *LC pointer to LinkedCell_deprecated structure
     1471 */
     1472void Tesselation::AddDegeneratedTriangle(CandidateForTesselation &CandidateLine, const double RADIUS, const LinkedCell_deprecated *LC)
    14731473{
    14741474  Info FunctionInfo(__func__);
    … …  
    18761876 * \param Storage[3] array storing angles and other candidate information
    18771877 * \param RADIUS radius of virtual sphere
    1878  * \param *LC LinkedCell structure with neighbouring points
    1879  */
    1880 void Tesselation::FindSecondPointForTesselation(TesselPoint* a, Vector Oben, TesselPoint*& OptCandidate, double Storage[3], double RADIUS, const LinkedCell *LC)
     1878 * \param *LC LinkedCell_deprecated structure with neighbouring points
     1879 */
     1880void Tesselation::FindSecondPointForTesselation(TesselPoint* a, Vector Oben, TesselPoint*& OptCandidate, double Storage[3], double RADIUS, const LinkedCell_deprecated *LC)
    18811881{
    18821882  Info FunctionInfo(__func__);
    … …  
    19841984 * @param ThirdPoint third point to avoid in search
    19851985 * @param RADIUS radius of sphere
    1986  * @param *LC LinkedCell structure with neighbouring points
    1987  */
    1988 void Tesselation::FindThirdPointForTesselation(const Vector &NormalVector, const Vector &SearchDirection, const Vector &OldSphereCenter, CandidateForTesselation &CandidateLine, const class BoundaryPointSet * const ThirdPoint, const double RADIUS, const LinkedCell *LC) const
     1986 * @param *LC LinkedCell_deprecated structure with neighbouring points
     1987 */
     1988void Tesselation::FindThirdPointForTesselation(const Vector &NormalVector, const Vector &SearchDirection, const Vector &OldSphereCenter, CandidateForTesselation &CandidateLine, const class BoundaryPointSet * const ThirdPoint, const double RADIUS, const LinkedCell_deprecated *LC) const
    19891989{
    19901990  Info FunctionInfo(__func__);
    … …  
    22192219 * \return map of BoundaryPointSet of closest points sorted by squared distance or NULL.
    22202220 */
    2221 DistanceToPointMap * Tesselation::FindClosestBoundaryPointsToVector(const Vector &x, const LinkedCell* LC) const
     2221DistanceToPointMap * Tesselation::FindClosestBoundaryPointsToVector(const Vector &x, const LinkedCell_deprecated* LC) const
    22222222{
    22232223  Info FunctionInfo(__func__);
    … …  
    22702270 * \return closest BoundaryLineSet or NULL in degenerate case.
    22712271 */
    2272 BoundaryLineSet * Tesselation::FindClosestBoundaryLineToVector(const Vector &x, const LinkedCell* LC) const
     2272BoundaryLineSet * Tesselation::FindClosestBoundaryLineToVector(const Vector &x, const LinkedCell_deprecated* LC) const
    22732273{
    22742274  Info FunctionInfo(__func__);
    … …  
    23302330 * \return BoundaryTriangleSet of nearest triangle or NULL.
    23312331 */
    2332 TriangleList * Tesselation::FindClosestTrianglesToVector(const Vector &x, const LinkedCell* LC) const
     2332TriangleList * Tesselation::FindClosestTrianglesToVector(const Vector &x, const LinkedCell_deprecated* LC) const
    23332333{
    23342334  Info FunctionInfo(__func__);
    … …  
    24172417 * \return list of BoundaryTriangleSet of nearest triangles or NULL.
    24182418 */
    2419 class BoundaryTriangleSet * Tesselation::FindClosestTriangleToVector(const Vector &x, const LinkedCell* LC) const
     2419class BoundaryTriangleSet * Tesselation::FindClosestTriangleToVector(const Vector &x, const LinkedCell_deprecated* LC) const
    24202420{
    24212421  Info FunctionInfo(__func__);
    … …  
    24522452 * Basically calls Tesselation::GetDistanceToSurface() and checks the sign of the return value.
    24532453 * @param point of which to check the position
    2454  * @param *LC LinkedCell structure
     2454 * @param *LC LinkedCell_deprecated structure
    24552455 *
    24562456 * @return true if the point is inside the Tesselation structure, false otherwise
    24572457 */
    2458 bool Tesselation::IsInnerPoint(const Vector &Point, const LinkedCell* const LC) const
     2458bool Tesselation::IsInnerPoint(const Vector &Point, const LinkedCell_deprecated* const LC) const
    24592459{
    24602460  Info FunctionInfo(__func__);
    … …  
    24792479 *
    24802480 * @param point of which to check the position
    2481  * @param *LC LinkedCell structure
     2481 * @param *LC LinkedCell_deprecated structure
    24822482 *
    24832483 * @return >0 if outside, ==0 if on surface, <0 if inside
    … …  
    25402540 * \return distance squared to closest point on surface
    25412541 */
    2542 double Tesselation::GetDistanceToSurface(const Vector &Point, const LinkedCell* const LC) const
     2542double Tesselation::GetDistanceToSurface(const Vector &Point, const LinkedCell_deprecated* const LC) const
    25432543{
    25442544  Info FunctionInfo(__func__);
    … …  
    25552555 * \return distance squared to closest point on surface
    25562556 */
    2557 BoundaryTriangleSet * Tesselation::GetClosestTriangleOnSurface(const Vector &Point, const LinkedCell* const LC) const
     2557BoundaryTriangleSet * Tesselation::GetClosestTriangleOnSurface(const Vector &Point, const LinkedCell_deprecated* const LC) const
    25582558{
    25592559  Info FunctionInfo(__func__);
    … …  
    35453545 * \param *LC Linked Cell structure to find nearest point
    35463546 */
    3547 void Tesselation::AddBoundaryPointByDegeneratedTriangle(class TesselPoint *point, LinkedCell *LC)
     3547void Tesselation::AddBoundaryPointByDegeneratedTriangle(class TesselPoint *point, LinkedCell_deprecated *LC)
    35483548{
    35493549  Info FunctionInfo(__func__);

  • src/Tesselation/tesselation.hpp

    rf55ae5 r6bd7e0  
    4040class CandidateForTesselation;
    4141class IPointCloud;
    42 class LinkedCell;
     42class LinkedCell_deprecated;
    4343class Plane;
    4444class Tesselation;
    … …  
    7878    void AddTesselationTriangle(const int nr);
    7979    void AddCandidateTriangle(CandidateForTesselation &CandidateLine, enum centers type);
    80     void AddDegeneratedTriangle(CandidateForTesselation &CandidateLine, const double RADIUS, const LinkedCell *LC);
    81     void AddCandidatePolygon(CandidateForTesselation CandidateLine, const double RADIUS, const LinkedCell *LC);
     80    void AddDegeneratedTriangle(CandidateForTesselation &CandidateLine, const double RADIUS, const LinkedCell_deprecated *LC);
     81    void AddCandidatePolygon(CandidateForTesselation CandidateLine, const double RADIUS, const LinkedCell_deprecated *LC);
    8282    void RemoveTesselationTriangle(class BoundaryTriangleSet *triangle);
    8383    void RemoveTesselationLine(class BoundaryLineSet *line);
    8484    void RemoveTesselationPoint(class BoundaryPointSet *point);
    85     bool CheckDegeneracy(CandidateForTesselation &CandidateLine, const double RADIUS, const LinkedCell *LC) const;
     85    bool CheckDegeneracy(CandidateForTesselation &CandidateLine, const double RADIUS, const LinkedCell_deprecated *LC) const;
    8686
    8787
    8888    // concave envelope
    89     bool FindStartingTriangle(const double RADIUS, const LinkedCell *LC);
    90     void FindSecondPointForTesselation(class TesselPoint* a, Vector Oben, class TesselPoint*& OptCandidate, double Storage[3], double RADIUS, const LinkedCell *LC);
    91     void FindThirdPointForTesselation(const Vector &NormalVector, const Vector &SearchDirection, const Vector &OldSphereCenter, CandidateForTesselation &CandidateLine, const class BoundaryPointSet  * const ThirdNode, const double RADIUS, const LinkedCell *LC) const;
    92     bool FindNextSuitableTriangle(CandidateForTesselation &CandidateLine, const BoundaryTriangleSet &T, const double& RADIUS, const LinkedCell *LC);
    93     bool FindCandidatesforOpenLines(const double RADIUS, const LinkedCell *&LCList);
     89    bool FindStartingTriangle(const double RADIUS, const LinkedCell_deprecated *LC);
     90    void FindSecondPointForTesselation(class TesselPoint* a, Vector Oben, class TesselPoint*& OptCandidate, double Storage[3], double RADIUS, const LinkedCell_deprecated *LC);
     91    void FindThirdPointForTesselation(const Vector &NormalVector, const Vector &SearchDirection, const Vector &OldSphereCenter, CandidateForTesselation &CandidateLine, const class BoundaryPointSet  * const ThirdNode, const double RADIUS, const LinkedCell_deprecated *LC) const;
     92    bool FindNextSuitableTriangle(CandidateForTesselation &CandidateLine, const BoundaryTriangleSet &T, const double& RADIUS, const LinkedCell_deprecated *LC);
     93    bool FindCandidatesforOpenLines(const double RADIUS, const LinkedCell_deprecated *&LCList);
    9494    int CheckPresenceOfTriangle(class TesselPoint *Candidates[3]) const;
    9595    class BoundaryTriangleSet * GetPresentTriangle(TesselPoint *Candidates[3]);
    … …  
    9898    void TesselateOnBoundary(IPointCloud & cloud);
    9999    void GuessStartingTriangle();
    100     bool InsertStraddlingPoints(IPointCloud & cloud, const LinkedCell *LC);
     100    bool InsertStraddlingPoints(IPointCloud & cloud, const LinkedCell_deprecated *LC);
    101101    double RemovePointFromTesselatedSurface(class BoundaryPointSet *point);
    102102    class BoundaryLineSet * FlipBaseline(class BoundaryLineSet *Base);
    … …  
    106106    IndexToIndex * FindAllDegeneratedLines();
    107107    void RemoveDegeneratedTriangles();
    108     void AddBoundaryPointByDegeneratedTriangle(class TesselPoint *point, LinkedCell *LC);
     108    void AddBoundaryPointByDegeneratedTriangle(class TesselPoint *point, LinkedCell_deprecated *LC);
    109109    int CorrectAllDegeneratedPolygons();
    110110
    … …  
    117117    class BoundaryPointSet * GetCommonEndpoint(const BoundaryLineSet * line1, const BoundaryLineSet * line2) const;
    118118    TriangleList * FindTriangles(const TesselPoint* const Points[3]) const;
    119     TriangleList * FindClosestTrianglesToVector(const Vector &x, const LinkedCell* LC) const;
    120     BoundaryTriangleSet * FindClosestTriangleToVector(const Vector &x, const LinkedCell* LC) const;
    121     bool IsInnerPoint(const Vector &Point, const LinkedCell* const LC) const;
     119    TriangleList * FindClosestTrianglesToVector(const Vector &x, const LinkedCell_deprecated* LC) const;
     120    BoundaryTriangleSet * FindClosestTriangleToVector(const Vector &x, const LinkedCell_deprecated* LC) const;
     121    bool IsInnerPoint(const Vector &Point, const LinkedCell_deprecated* const LC) const;
    122122    double GetDistanceSquaredToTriangle(const Vector &Point, const BoundaryTriangleSet* const triangle) const;
    123     double GetDistanceToSurface(const Vector &Point, const LinkedCell* const LC) const;
    124     BoundaryTriangleSet * GetClosestTriangleOnSurface(const Vector &Point, const LinkedCell* const LC) const;
     123    double GetDistanceToSurface(const Vector &Point, const LinkedCell_deprecated* const LC) const;
     124    BoundaryTriangleSet * GetClosestTriangleOnSurface(const Vector &Point, const LinkedCell_deprecated* const LC) const;
    125125    bool AddBoundaryPoint(TesselPoint * Walker, const int n);
    126     DistanceToPointMap * FindClosestBoundaryPointsToVector(const Vector &x, const LinkedCell* LC) const;
    127     BoundaryLineSet * FindClosestBoundaryLineToVector(const Vector &x, const LinkedCell* LC) const;
     126    DistanceToPointMap * FindClosestBoundaryPointsToVector(const Vector &x, const LinkedCell_deprecated* LC) const;
     127    BoundaryLineSet * FindClosestBoundaryLineToVector(const Vector &x, const LinkedCell_deprecated* LC) const;
    128128
    129129    // print for debugging
    … …  
    163163    mutable PointMap::const_iterator InternalPointer;
    164164
    165     //bool HasOtherBaselineBetterCandidate(const BoundaryLineSet * const BaseRay, const TesselPoint * const OptCandidate, double ShortestAngle, double RADIUS, const LinkedCell * const LC) const;
     165    //bool HasOtherBaselineBetterCandidate(const BoundaryLineSet * const BaseRay, const TesselPoint * const OptCandidate, double ShortestAngle, double RADIUS, const LinkedCell_deprecated * const LC) const;
    166166    void FindDegeneratedCandidatesforOpenLines(TesselPoint * const Sprinter, const Vector * const OptCenter);
    167167};

  • src/Tesselation/tesselationhelpers.cpp

    rf55ae5 r6bd7e0  
    409409 * @return point which is second closest to the provided one
    410410 */
    411 TesselPoint* FindSecondClosestTesselPoint(const Vector& Point, const LinkedCell* const LC)
     411TesselPoint* FindSecondClosestTesselPoint(const Vector& Point, const LinkedCell_deprecated* const LC)
    412412{
    413413        Info FunctionInfo(__func__);
    … …  
    461461 * @return point which is closest to the provided one, NULL if none found
    462462 */
    463 TesselPoint* FindClosestTesselPoint(const Vector& Point, TesselPoint *&SecondPoint, const LinkedCell* const LC)
     463TesselPoint* FindClosestTesselPoint(const Vector& Point, TesselPoint *&SecondPoint, const LinkedCell_deprecated* const LC)
    464464{
    465465        Info FunctionInfo(__func__);

  • src/Tesselation/tesselationhelpers.hpp

    rf55ae5 r6bd7e0  
    3232class BoundaryPolygonSet;
    3333class CandidateForTesselation;
    34 class LinkedCell;
     34class LinkedCell_deprecated;
    3535class TesselPoint;
    3636class IPointCloud;
    … …  
    5252bool CheckLineCriteriaForDegeneratedTriangle(const BoundaryPointSet * const nodes[3]);
    5353bool SortCandidates(const CandidateForTesselation* candidate1, const CandidateForTesselation *candidate2);
    54 TesselPoint* FindClosestTesselPoint(const Vector & Point, TesselPoint *&SecondPoint, const LinkedCell* const LC);
    55 TesselPoint* FindSecondClosestTesselPoint(const Vector &, const LinkedCell* const LC);
     54TesselPoint* FindClosestTesselPoint(const Vector & Point, TesselPoint *&SecondPoint, const LinkedCell_deprecated* const LC);
     55TesselPoint* FindSecondClosestTesselPoint(const Vector &, const LinkedCell_deprecated* const LC);
    5656Vector * GetClosestPointBetweenLine(const BoundaryLineSet * const Base, const BoundaryLineSet * const OtherBase);
    5757

  • src/Tesselation/triangleintersectionlist.cpp

    rf55ae5 r6bd7e0  
    4141 *
    4242 */
    43 TriangleIntersectionList::TriangleIntersectionList(const Vector &x, const Tesselation *surface, const LinkedCell* LC) :
     43TriangleIntersectionList::TriangleIntersectionList(const Vector &x, const Tesselation *surface, const LinkedCell_deprecated* LC) :
    4444  Point(x),
    4545  Tess(surface),

  • src/Tesselation/triangleintersectionlist.hpp

    rf55ae5 r6bd7e0  
    2323
    2424class BoundaryTriangleSet;
    25 class LinkedCell;
     25class LinkedCell_deprecated;
    2626class Tesselation;
    2727class Vector;
    … …  
    3939{
    4040public:
    41   TriangleIntersectionList(const Vector &x, const Tesselation *surface, const LinkedCell* LC);
     41  TriangleIntersectionList(const Vector &x, const Tesselation *surface, const LinkedCell_deprecated* LC);
    4242  ~TriangleIntersectionList();
    4343
    … …  
    5454  const Vector &Point;
    5555  const Tesselation *Tess;
    56   const LinkedCell *Vicinity;
     56  const LinkedCell_deprecated *Vicinity;
    5757  TriangleVectorMap IntersectionList;
    5858  mutable DistanceTriangleMap DistanceList;

  • src/Tesselation/unittests/TesselationUnitTest.cpp

    rf55ae5 r6bd7e0  
    7575  // create linkedcell
    7676  PointCloudAdaptor<TesselPointSTLList> cloud(&Corners, "TesselPointSTLList");
    77   LinkedList = new LinkedCell(cloud, 2.*SPHERERADIUS);
     77  LinkedList = new LinkedCell_deprecated(cloud, 2.*SPHERERADIUS);
    7878
    7979  // create tesselation

  • src/Tesselation/unittests/TesselationUnitTest.hpp

    rf55ae5 r6bd7e0  
    4343      class Tesselation *TesselStruct;
    4444      TesselPointSTLList Corners;
    45       class LinkedCell *LinkedList;
     45      class LinkedCell_deprecated *LinkedList;
    4646};
    4747

  • src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp

    rf55ae5 r6bd7e0  
    9898  // create linkedcell
    9999  PointCloudAdaptor< TesselPointSTLList > cloud(&Corners, "TesselPointSTLList");
    100   LinkedList = new LinkedCell(cloud, 2.*SPHERERADIUS);
     100  LinkedList = new LinkedCell_deprecated(cloud, 2.*SPHERERADIUS);
    101101
    102102  // create tesselation

  • src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.hpp

    rf55ae5 r6bd7e0  
    4040      class Tesselation *TesselStruct;
    4141      TesselPointSTLList Corners;
    42       class LinkedCell *LinkedList;
     42      class LinkedCell_deprecated *LinkedList;
    4343};
    4444

  • src/molecule.hpp

    rf55ae5 r6bd7e0  
    4848class ForceMatrix;
    4949class Graph;
    50 class LinkedCell;
     50class LinkedCell_deprecated;
    5151class molecule;
    5252class MoleculeLeafClass;
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