Changeset a1c8fa for src


Ignore:
Timestamp:
Oct 20, 2016, 8:54:23 PM (9 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChronosMutex, Fix_ForceAnnealing, Fix_ParseParticles, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable
Children:
72e40d0
Parents:
064b34
git-author:
Frederik Heber <heber@…> (09/27/16 09:58:43)
git-committer:
Frederik Heber <heber@…> (10/20/16 20:54:23)
Message:

FIX: BondedParticleInfo::MaxOrder and ::AdapativeOrder are now stored per trajectory step.

  • adapted uses in AdaptivityMap and Fragmentation as members are now protected.
Location:
src
Files:
6 edited

Legend:

Unmodified
Added
Removed

  • src/Atom/atom_bondedparticle.cpp

    r064b34 ra1c8fa  
    7171void BondedParticle::OutputOrder(ofstream *file) const
    7272{
    73   *file << getNr() << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << endl;
    74   //LOG(2, "Storing: " << getNr() << "\t" << (int)AdaptiveOrder << "\t" << MaxOrder << ".");
     73  *file << getNr() << "\t" << (int)getAdaptiveOrder() << "\t" << (int)getMaxOrder() << endl;
     74  //LOG(2, "Storing: " << getNr() << "\t" << (int)getAdaptiveOrder() << "\t" << getMaxOrder() << ".");
    7575};
    7676

  • src/Atom/atom_bondedparticleinfo.cpp

    r064b34 ra1c8fa  
    4545BondList BondedParticleInfo::emptyList;
    4646
    47 /** Constructor of class BondedParticleInfo.
    48  */
    49 BondedParticleInfo::BondedParticleInfo() :
    50   AdaptiveOrder(0),
    51   MaxOrder(0)
    52 {}
    53 
    54 /** Destructor of class BondedParticleInfo.
    55  */
    56 BondedParticleInfo::~BondedParticleInfo()
    57 {}
    58 
    5947void BondedParticleInfo::AppendTrajectoryStep(const unsigned int _step)
    6048{
    … …  
    7462}
    7563
     64template <class List_t>
     65void setEntryInList(
     66    List_t &_list,
     67    const typename List_t::key_type _step,
     68    const typename List_t::mapped_type &_value)
     69{
     70  typename List_t::iterator iter =
     71    _list.find(_step);
     72  if (iter != _list.end())
     73    iter->second = _value;
     74  else
     75    _list.insert( std::make_pair(_step, _value) );
     76}
     77
     78template <class List_t>
     79const typename List_t::mapped_type& getEntryInList(
     80    const List_t &_list,
     81    const typename List_t::key_type _step,
     82    const typename List_t::mapped_type &_empty)
     83{
     84  typename List_t::const_iterator iter =
     85    _list.find(_step);
     86  if (iter != _list.end())
     87    return iter->second;
     88  return _empty;
     89}
     90
    7691const BondList& BondedParticleInfo::getListOfBondsAtStep(unsigned int _step) const
    7792{
    78   BondTrajectory_t::const_iterator iter =
    79     ListOfBonds.find(_step);
    80   if (iter != ListOfBonds.end())
    81     return iter->second;
    82   return emptyList;
     93  return getEntryInList<BondTrajectory_t>(ListOfBonds, _step, emptyList);
    8394}
     95
     96const unsigned char& BondedParticleInfo::getMaxOrder() const
     97{
     98  return getMaxOrder(WorldTime::getTime());
     99}
     100
     101const unsigned char& BondedParticleInfo::getMaxOrder(unsigned int _step) const
     102{
     103  static unsigned char emptyOrder=0;
     104  return getEntryInList<OrderTrajectory_t>(MaxOrder, _step, emptyOrder);
     105}
     106
     107void BondedParticleInfo::setMaxOrder(unsigned char _value)
     108{
     109  setMaxOrder(WorldTime::getTime(), _value);
     110}
     111
     112void BondedParticleInfo::setMaxOrder(unsigned int _step, const unsigned char _value)
     113{
     114  setEntryInList<OrderTrajectory_t>(MaxOrder, _step, _value);
     115}
     116
     117const unsigned char& BondedParticleInfo::getAdaptiveOrder() const
     118{
     119  return getAdaptiveOrder(WorldTime::getTime());
     120}
     121
     122const unsigned char& BondedParticleInfo::getAdaptiveOrder(unsigned int _step) const
     123{
     124  static unsigned char emptyOrder=0;
     125  return getEntryInList<OrderTrajectory_t>(AdaptiveOrder, _step, emptyOrder);
     126}
     127
     128void BondedParticleInfo::setAdaptiveOrder(unsigned char _value)
     129{
     130  setAdaptiveOrder(WorldTime::getTime(), _value);
     131}
     132
     133void BondedParticleInfo::setAdaptiveOrder(unsigned int _step, const unsigned char _value)
     134{
     135  setEntryInList<OrderTrajectory_t>(AdaptiveOrder, _step, _value);
     136}
     137

  • src/Atom/atom_bondedparticleinfo.hpp

    r064b34 ra1c8fa  
    3737  friend class BondedParticle;
    3838public:
    39   unsigned char AdaptiveOrder;  //!< current present bond order at site (0 means "not set")
    40   unsigned char MaxOrder;  //!< desired maximum order of this atom (0 means "not set")
    4139
    42   BondedParticleInfo();
    43   virtual ~BondedParticleInfo();
     40  virtual ~BondedParticleInfo() {}
    4441
    4542  /** Pushes back another step in all trajectory vectors.
    … …  
    6562  const BondList& getListOfBonds() const;
    6663
    67   /** Accessor to ListOfBonds of WorldTime::CurrentTime.
    68    *
    69    * Note, new empty BondList is returned if array entry at upper boundary is
    70    * accessed. Beyond std will issue exception due to out-of-range access.
    71    *
    72    * @return ListOfBonds[WorldTime::CurrentTime]
    73    */
    74 //  BondList& getListOfBonds();
    75 
    7664  /** Const Accessor ListOfBonds of any present time step.
    7765   *
    … …  
    8169  const BondList& getListOfBondsAtStep(unsigned int _step) const;
    8270
    83   /** Accessor ListOfBonds of any present time step.
     71  /** Const getter for the MaxOrder property at current time step.
    8472   *
    85    * Note, new empty BondList is returned if array entry at upper boundary is
    86    * accessed. Beyond std will issue exception due to out-of-range access.
     73   * @return MaxOrder[Current world time step].
     74   */
     75  const unsigned char& getMaxOrder() const;
     76
     77  /** Const getter for the MaxOrder property at given \a _step.
    8778   *
    8879   * @param _step time step to access
    89    * @return ListOfBonds[_step].
     80   * @return MaxOrder[_step].
    9081   */
    91 //  BondList& getListOfBondsAtStep(unsigned int _step);
     82  const unsigned char& getMaxOrder(const unsigned int _step) const;
     83
     84  /** Setter for the MaxOrder property at current time step.
     85   *
     86   * @param _value value to set for MaxOrder at current time step
     87   */
     88  void setMaxOrder(const unsigned char _value);
     89
     90  /**Setter for the MaxOrder property at given \a _step.
     91   *
     92   * @param _step time step to access
     93   * @param _value value to set for MaxOrder at the desired time step
     94   * @return MaxOrder[_step].
     95   */
     96  void setMaxOrder(const unsigned int _step, const unsigned char _value);
     97
     98  /** Const getter for the AdaptiveOrder property at current time step.
     99   *
     100   * @return AdaptiveOrder[Current world time step].
     101   */
     102  const unsigned char& getAdaptiveOrder() const;
     103
     104  /** Const getter for the AdaptiveOrder property at given \a _step.
     105   *
     106   * @param _step time step to access
     107   * @return AdaptiveOrder[_step].
     108   */
     109  const unsigned char& getAdaptiveOrder(const unsigned int _step) const;
     110
     111  /** Setter for the AdaptiveOrder property at current time step.
     112   *
     113   * @param _value value to set for AdaptiveOrder at current time step
     114   */
     115  void setAdaptiveOrder(const unsigned char _value);
     116
     117  /** Setter for the AdaptiveOrder property at given \a _step.
     118   *
     119   * @param _step time step to access
     120   * @param _value value to set for AdaptiveOrder at the desired time step
     121   * @return AdaptiveOrder[_step].
     122   */
     123  void setAdaptiveOrder(const unsigned int _step, const unsigned char _value);
    92124
    93125protected:
    … …  
    105137  BondTrajectory_t ListOfBonds; //!< list of all bonds
    106138  static BondList emptyList;  //!< empty list to return when step is not present
     139
     140  typedef std::map<unsigned int, unsigned char> OrderTrajectory_t;
     141  OrderTrajectory_t AdaptiveOrder;  //!< current present bond order at site (0 means "not set")
     142  OrderTrajectory_t MaxOrder;  //!< desired maximum order of this atom (0 means "not set")
    107143};
    108144

  • src/Fragmentation/AdaptivityMap.cpp

    r064b34 ra1c8fa  
    154154    Walker = mol->FindAtom((*runner).first);
    155155    if (Walker != NULL) {
    156       //if ((*runner).second.second >= Walker->AdaptiveOrder) { // only insert if this is an "active" root site for the current order
    157       if (Walker->MaxOrder > Walker->AdaptiveOrder) {
     156      //if ((*runner).second.second >= Walker->getAdaptiveOrder()) { // only insert if this is an "active" root site for the current order
     157      if (Walker->getMaxOrder() > Walker->getAdaptiveOrder()) {
    158158        LOG(2, "(" << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "])");
    159159        FinalRootCandidates->insert( make_pair( (*runner).second.first, pair<int,int>((*runner).first, (*runner).second.second) ) );

  • src/Fragmentation/Fragmentation.cpp

    r064b34 ra1c8fa  
    286286    atom *Walker = mol->FindAtom(RootKeyNr);
    287287    // check cyclic lengths
    288     //if ((MinimumRingSize[Walker->GetTrueFather()->getNr()] != -1) && (Walker->GetTrueFather()->AdaptiveOrder+1 > MinimumRingSize[Walker->GetTrueFather()->getNr()])) {
    289     //  LOG(0, "Bond order " << Walker->GetTrueFather()->AdaptiveOrder << " of Root " << *Walker << " greater than or equal to Minimum Ring size of " << MinimumRingSize << " found is not allowed.");
     288    //if ((MinimumRingSize[Walker->GetTrueFather()->getNr()] != -1) && (Walker->GetTrueFather()->getAdaptiveOrder()+1 > MinimumRingSize[Walker->GetTrueFather()->getNr()])) {
     289    //  LOG(0, "Bond order " << Walker->GetTrueFather()->getAdaptiveOrder() << " of Root " << *Walker << " greater than or equal to Minimum Ring size of " << MinimumRingSize << " found is not allowed.");
    290290    //} else
    291291    {
    292292      // set adaptive order to desired max order
    293       Walker->GetTrueFather()->AdaptiveOrder = Walker->GetTrueFather()->MaxOrder;
    294       Order = Walker->AdaptiveOrder = Walker->GetTrueFather()->AdaptiveOrder;
     293      Walker->GetTrueFather()->setAdaptiveOrder(Walker->GetTrueFather()->getMaxOrder());
     294      Order = Walker->GetTrueFather()->getAdaptiveOrder();
     295      Walker->setAdaptiveOrder(Order);
    295296
    296297      // allocate memory for all lower level orders
    … …  
    302303      // initialise Order-dependent entries of UniqueFragments structure
    303304      UniqueFragments FragmentSearch(1., FragmentLowerOrdersList[RootNr], Walker);
    304       PowerSetGenerator PSG(&FragmentSearch, Walker->AdaptiveOrder);
     305      PowerSetGenerator PSG(&FragmentSearch, Walker->getAdaptiveOrder());
    305306
    306307      // create top order where nothing is reduced
    … …  
    316317//        NumMolecules = 0;
    317318//      }
    318       // now, we have completely filled each cell of FragmentLowerOrdersList[] for the current Walker->AdaptiveOrder
    319       //NumMoleculesOfOrder[Walker->AdaptiveOrder-1] = NumMolecules;
     319      // now, we have completely filled each cell of FragmentLowerOrdersList[] for the current Walker->getAdaptiveOrder()
     320      //NumMoleculesOfOrder[Walker->getAdaptiveOrder()-1] = NumMolecules;
    320321      TotalNumMolecules += NumMoleculesOfOrder[RootNr];
    321 //      LOG(1, "Number of resulting molecules for Order " << (int)Walker->GetTrueFather()->AdaptiveOrder << " is: " << NumMoleculesOfOrder[RootNr] << ".");
     322//      LOG(1, "Number of resulting molecules for Order " << (int)Walker->GetTrueFather()->getAdaptiveOrder() << " is: " << NumMoleculesOfOrder[RootNr] << ".");
    322323      RootStack.push_back(RootKeyNr); // put back on stack
    323324      RootNr++;
    … …  
    407408      atom * const Walker = *iter;
    408409      if (AtomMask.isTrue(Walker->getNr())) { // skip masked out
    409         Walker->MaxOrder = (Order != 0 ? Order : Walker->MaxOrder+1);
     410        Walker->setMaxOrder((Order != 0 ? Order : Walker->getMaxOrder()+1));
    410411        // remove all that have reached desired order
    411         if (Walker->AdaptiveOrder >= Walker->MaxOrder) // && (Walker->AdaptiveOrder < MinimumRingSize[Walker->getNr()]))
     412        if (Walker->getAdaptiveOrder() >= Walker->getMaxOrder()) // && (Walker->getAdaptiveOrder() < MinimumRingSize[Walker->getNr()]))
    412413          AtomMask.setFalse(Walker->getNr());
    413414        else
    … …  
    451452        ++iter) {
    452453      file << (*iter)->getId()
    453           << "\t" << (int)(*iter)->AdaptiveOrder
    454           << "\t" << (int)(*iter)->MaxOrder << std::endl;
     454          << "\t" << (int)(*iter)->getAdaptiveOrder()
     455          << "\t" << (int)(*iter)->getMaxOrder() << std::endl;
    455456    }
    456457    file.close();
    … …  
    513514    // set atom values
    514515    for(molecule::iterator iter=mol->begin();iter!=mol->end();++iter){
    515       (*iter)->AdaptiveOrder = OrderArray[(*iter)->getNr()];
    516       (*iter)->MaxOrder = OrderArray[(*iter)->getNr()]; //MaxArray.isTrue((*iter)->getNr());
     516      (*iter)->setAdaptiveOrder(OrderArray[(*iter)->getNr()]);
     517      (*iter)->setMaxOrder(OrderArray[(*iter)->getNr()]); //MaxArray.isTrue((*iter)->getNr());
    517518    }
    518519    //SetAtomValueToIndexedArray( OrderArray, &atom::getNr(), &atom::AdaptiveOrder );

  • src/Fragmentation/fragmentation_helpers.cpp

    r064b34 ra1c8fa  
    4545
    4646#include "Atom/atom.hpp"
    47 #include "Fragmentation/AdaptivityMap.hpp"
    4847#include "Fragmentation/AtomMask.hpp"
    4948#include "Fragmentation/Graph.hpp"
    … …  
    103102    RootStack.pop_front();
    104103    Walker = mol->FindAtom(RootKeyNr);
    105     NumLevels = Walker->AdaptiveOrder;
     104    NumLevels = Walker->getAdaptiveOrder();
    106105    ASSERT( NumLevels == FragmentLowerOrdersList[RootNr].size(),
    107106        "CombineAllOrderListIntoOne() - differing size and NumLevels.");
    … …  
    134133    RootStack.pop_front();
    135134    Walker = mol->FindAtom(RootKeyNr);
    136     NumLevels = Walker->AdaptiveOrder;
     135    NumLevels = Walker->getAdaptiveOrder();
    137136    for(int i=0;i<NumLevels;i++) {
    138137      if (FragmentLowerOrdersList[RootNr][i] != NULL) {
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