Changeset 53d894 for src/LinkedCell


Ignore:
Timestamp:
Jan 2, 2012, 1:34:29 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:
4834f4
Parents:
c80643
git-author:
Frederik Heber <heber@…> (12/19/11 21:50:54)
git-committer:
Frederik Heber <heber@…> (01/02/12 13:34:29)
Message:

Changed LinkedCell_Model::getNeighborhoodBounds() and LinkedCell_View::getAllNeighbors().

  • NeighborhoodBounds are now index and offset style, not two real bounds anymore. This way we were able to get getAllNeighbors() actually working.
  • getNeighborhoodBounds() was overloaded nonsense for Bounce case, it is now much simpler: we just crop the interval at the boundary.
Location:
src/LinkedCell
Files:
3 edited

Legend:

Unmodified
Added
Removed

  • src/LinkedCell/LinkedCell_Model.cpp

    rc80643 r53d894  
    351351      break;
    352352    case Box::Bounce:
     353      if (index[i] < 0)
     354        index[i] = 0;
     355      if (index[i] >= getSize(i))
     356        index[i] = getSize(i)-1;
    353357      break;
    354358    case Box::Ignore:
     359      if (index[i] < 0)
     360        index[i] = 0;
     361      if (index[i] >= getSize(i))
     362        index[i] = getSize(i)-1;
    355363      break;
    356364    default:
    … …  
    362370
    363371/** Calculates the interval bounds of the linked cell grid.
     372 *
     373 * \note we assume for index to allows be valid, i.e. within the range of LinkedCell_Model::N.
     374 *
    364375 * \param index index to give relative bounds to
    365376 * \param step how deep to check the neighbouring cells (i.e. number of layers to check)
    … …  
    375386  // calculate bounds
    376387  for (size_t i=0;i<NDIM;++i) {
     388    ASSERT(index[i] >= 0,
     389        "LinkedCell_Model::getNeighborhoodBounds() - index "+toString(index)+" out of lower bounds.");
     390    ASSERT (index[i] < getSize(i),
     391        "LinkedCell_Model::getNeighborhoodBounds() - index "+toString(index)+" out of upper bounds.");
    377392    switch (domain.getConditions()[i]) {
    378393      case Box::Wrap:
     394        if ((index[i] - step[i]) < 0)
     395          neighbors.first[i] = getSize(i) + (index[i] - step[i]);
     396        else if ((index[i] - step[i]) >= getSize(i))
     397          neighbors.first[i] = (index[i] - step[i]) - getSize(i);
     398        else
     399          neighbors.first[i] = index[i] - step[i];
     400        neighbors.second[i] = 2*step[i]+1;
     401        break;
     402      case Box::Bounce:
     403        neighbors.second[i] = 2*step[i]+1;
    379404        if (index[i] - step[i] >= 0) {
    380405          neighbors.first[i] = index[i] - step[i];
    381406        } else {
    382           neighbors.first[i] = getSize(i) - (index[i] - step[i]);
     407          neighbors.first[i] = 0;
     408          neighbors.second[i] = index[i] + step[i]+1;
    383409        }
    384         if (index[i] + step[i] < getSize(i)) {
    385           neighbors.second[i] = index[i] + step[i];
    386         } else {
    387           neighbors.second[i] = index[i] + step[i] - getSize(i);
     410        if (index[i] + step[i] >= getSize(i)) {
     411          neighbors.second[i] = getSize(i) - (index[i] - step[i]);
    388412        }
    389413        break;
    390       case Box::Bounce:
    391         if (index[i] - step[i] >= 0) {
     414      case Box::Ignore:
     415        if (index[i] - step[i] < 0)
     416          neighbors.first[i] = 0;
     417        else
    392418          neighbors.first[i] = index[i] - step[i];
    393         } else {
    394           neighbors.first[i] = - (index[i] - step[i]);
    395         }
    396         if (index[i] + step[i] < getSize(i)) {
    397           neighbors.second[i] = index[i] + step[i];
    398         } else {
    399           const size_t shift = index[i] + step[i];
    400           const size_t mod = shift / getSize(i);
    401           if ((mod / 2)*2 == mod) // even -> come in from lower bound
    402             neighbors.second[i] = (shift % getSize(i));
    403           else // odd -> come in from upper bound
    404             neighbors.second[i] = getSize(i) - (shift % getSize(i));
    405         }
    406         break;
    407       case Box::Ignore:
    408         ASSERT(index[i] - step[i] >= 0,
    409             "LinkedCell_Model::getNeighborhoodBounds() - lower out of bounds on 'Ignore' boundary conditions");
    410         neighbors.first[i] = index[i] - step[i];
    411         ASSERT (index[i] + step[i] < getSize(i),
    412             "LinkedCell_Model::getNeighborhoodBounds() - upper out of bounds on 'Ignore' boundary conditions");
    413         neighbors.second[i] = index[i] + step[i];
    414         ASSERT(neighbors.second[i] < neighbors.first[i],
    415             "LinkedCell_Model::getNeighborhoodBounds() - ["
    416             +toString(neighbors.first[i])+","+toString(neighbors.second[i])
    417             +"] does not make sense as array bounds.");
     419        if (index[i] + step[i] >= getSize(i))
     420          neighbors.second[i] = getSize(i) - index[i];
     421        else
     422          neighbors.second[i] = 2*step[i]+1;
    418423        break;
    419424      default:

  • src/LinkedCell/LinkedCell_Model.hpp

    rc80643 r53d894  
    6060    bool checkArrayBounds(const tripleIndex &index) const;
    6161    void applyBoundaryConditions(tripleIndex &index) const;
     62    bool empty() const { return CellLookup.size() == 0; }
    6263
    6364    void addNode(const TesselPoint *Walker);

  • src/LinkedCell/LinkedCell_View.cpp

    rc80643 r53d894  
    2222#include "LinkedCell_View.hpp"
    2323
     24#include "CodePatterns/Log.hpp"
     25
    2426#include "Atom/TesselPoint.hpp"
    2527#include "LinearAlgebra/Vector.hpp"
    … …  
    3739{
    3840}
     41
    3942
    4043/** Return at least as many points as are inside a sphere of \a radius around \a center.
    … …  
    5760
    5861  tripleIndex n;
    59   for (n[0] = neighbors.first[0]; n[0] <= neighbors.second[0]; n[0]++)
    60     for (n[1] = neighbors.first[1]; n[1] <= neighbors.second[1]; n[1]++)
    61       for (n[2] = neighbors.first[2]; n[2] <= neighbors.second[2]; n[2]++) {
    62         if (!LC.checkArrayBounds(n))
    63           LC.applyBoundaryConditions(n);
    64         const LinkedCell &List = LC.getCell(n);
    65         //LOG(1, "Current cell is " << n[0] << ", " << n[1] << ", " << n[2] << " with No. " << index << ".");
     62  for (n[0] = 0; n[0] < neighbors.second[0]; n[0]++)
     63    for (n[1] = 0; n[1] < neighbors.second[1]; n[1]++)
     64      for (n[2] = 0; n[2] < neighbors.second[2]; n[2]++) {
     65        tripleIndex absolute_n = neighbors.first + n;
     66        if (!LC.checkArrayBounds(absolute_n))
     67          LC.applyBoundaryConditions(absolute_n);
     68        const LinkedCell &List = LC.getCell(absolute_n);
     69        LOG(1, "Current cell is " << neighbors.first << " plus " << n << ", yielding " << absolute_n << ".");
    6670        for (LinkedCell::const_iterator Runner = List.begin(); Runner != List.end(); Runner++)
    6771          TesselList.push_back(*Runner);
    … …  
    8488  return ReturnList;
    8589}
    86 
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