source: src/Fragmentation/fragmentation_helpers.cpp@ 730d7a

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010 University of Bonn. All rights reserved.
 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
 */

/*
 * fragmentation_helpers.cpp
 *
 *  Created on: Oct 18, 2011
 *      Author: heber
 */

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "CodePatterns/MemDebug.hpp"

#include "fragmentation_helpers.hpp"

#include <sstream>

#include "CodePatterns/Log.hpp"

#include "atom.hpp"
#include "Bond/bond.hpp"
#include "Element/element.hpp"
#include "Fragmentation/AdaptivityMap.hpp"
#include "Fragmentation/Graph.hpp"
#include "Fragmentation/KeySet.hpp"
#include "Helpers/defs.hpp"
#include "Helpers/helpers.hpp"
#include "molecule.hpp"

using namespace std;




/** Marks all candidate sites for update if below adaptive threshold.
 * Picks a given number of highest values and set *AtomMask to true.
 * \param *out output stream for debugging
 * \param *AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
 * \param FinalRootCandidates list candidates to check
 * \param Order desired order
 * \param *mol molecule with atoms
 * \return true - if update is necessary, false - not
 */
bool MarkUpdateCandidates(bool *AtomMask, std::map<double, std::pair<int,int> > &FinalRootCandidates, int Order, molecule *mol)
{
  atom *Walker = NULL;
  int No = -1;
  bool status = false;
  for(map<double, pair<int,int> >::iterator runner = FinalRootCandidates.upper_bound(pow(10.,Order)); runner != FinalRootCandidates.end(); runner++) {
    No = (*runner).second.first;
    Walker = mol->FindAtom(No);
    //if (Walker->AdaptiveOrder < MinimumRingSize[Walker->getNr()]) {
      DoLog(2) && (Log() << Verbose(2) << "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", setting entry " << No << " of Atom mask to true." << endl);
      AtomMask[No] = true;
      status = true;
    //} else
      //Log() << Verbose(2) << "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", however MinimumRingSize of " << MinimumRingSize[Walker->getNr()] << " does not allow further adaptive increase." << endl;
  }
  return status;
};

/** print atom mask for debugging.
 * \param *out output stream for debugging
 * \param *AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
 * \param AtomCount number of entries in \a *AtomMask
 */
void PrintAtomMask(bool *AtomMask, int AtomCount)
{
  DoLog(2) && (Log() << Verbose(2) << "              ");
  for(int i=0;i<AtomCount;i++)
    DoLog(0) && (Log() << Verbose(0) << (i % 10));
  DoLog(0) && (Log() << Verbose(0) << endl);
  DoLog(2) && (Log() << Verbose(2) << "Atom mask is: ");
  for(int i=0;i<AtomCount;i++)
    DoLog(0) && (Log() << Verbose(0) << (AtomMask[i] ? "t" : "f"));
  DoLog(0) && (Log() << Verbose(0) << endl);
};

/** Combines all KeySets from all orders into single ones (with just unique entries).
 * \param *out output stream for debugging
 * \param *&FragmentList list to fill
 * \param ***FragmentLowerOrdersList
 * \param &RootStack stack with all root candidates (unequal to each atom in complete molecule if adaptive scheme is applied)
 * \param *mol molecule with atoms and bonds
 */
int CombineAllOrderListIntoOne(Graph *&FragmentList, Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
{
  int RootNr = 0;
  int RootKeyNr = 0;
  int StartNr = 0;
  int counter = 0;
  int NumLevels = 0;
  atom *Walker = NULL;

  DoLog(0) && (Log() << Verbose(0) << "Combining the lists of all orders per order and finally into a single one." << endl);
  if (FragmentList == NULL) {
    FragmentList = new Graph;
    counter = 0;
  } else {
    counter = FragmentList->size();
  }

  StartNr = RootStack.back();
  do {
    RootKeyNr = RootStack.front();
    RootStack.pop_front();
    Walker = mol->FindAtom(RootKeyNr);
    NumLevels = 1 << (Walker->AdaptiveOrder - 1);
    for(int i=0;i<NumLevels;i++) {
      if (FragmentLowerOrdersList[RootNr][i] != NULL) {
        (*FragmentList).InsertGraph((*FragmentLowerOrdersList[RootNr][i]), &counter);
      }
    }
    RootStack.push_back(Walker->getNr());
    RootNr++;
  } while (RootKeyNr != StartNr);
  return counter;
};

/** Free's memory allocated for all KeySets from all orders.
 * \param *out output stream for debugging
 * \param ***FragmentLowerOrdersList
 * \param &RootStack stack with all root candidates (unequal to each atom in complete molecule if adaptive scheme is applied)
 * \param *mol molecule with atoms and bonds
 */
void FreeAllOrdersList(Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
{
  DoLog(1) && (Log() << Verbose(1) << "Free'ing the lists of all orders per order." << endl);
  int RootNr = 0;
  int RootKeyNr = 0;
  int NumLevels = 0;
  atom *Walker = NULL;
  while (!RootStack.empty()) {
    RootKeyNr = RootStack.front();
    RootStack.pop_front();
    Walker = mol->FindAtom(RootKeyNr);
    NumLevels = 1 << (Walker->AdaptiveOrder - 1);
    for(int i=0;i<NumLevels;i++) {
      if (FragmentLowerOrdersList[RootNr][i] != NULL) {
        delete(FragmentLowerOrdersList[RootNr][i]);
      }
    }
    delete[](FragmentLowerOrdersList[RootNr]);
    RootNr++;
  }
  delete[](FragmentLowerOrdersList);
};