source: src/Fragmentation/fragmentation_helpers.cpp@ 75363b

/*
 * 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/Graph.hpp"
#include "Fragmentation/KeySet.hpp"
#include "Helpers/defs.hpp"
#include "Helpers/helpers.hpp"
#include "molecule.hpp"

using namespace std;

/** Inserts a (\a No, \a value) pair into the list, overwriting present one.
 * Note if values are equal, No will decided on which is first
 * \param *out output stream for debugging
 * \param &AdaptiveCriteriaList list to insert into
 * \param &IndexedKeySetList list to find key set for a given index \a No
 * \param FragOrder current bond order of fragment
 * \param No index of keyset
 * \param value energy value
 */
void InsertIntoAdaptiveCriteriaList(std::map<int, pair<double,int> > *AdaptiveCriteriaList, std::map<int,KeySet> &IndexKeySetList, int FragOrder, int No, double Value)
{
  map<int,KeySet>::iterator marker = IndexKeySetList.find(No);    // find keyset to Frag No.
  if (marker != IndexKeySetList.end()) {  // if found
    Value *= 1 + MYEPSILON*(*((*marker).second.begin()));     // in case of equal energies this makes them not equal without changing anything actually
    // as the smallest number in each set has always been the root (we use global id to keep the doubles away), seek smallest and insert into AtomMask
    pair <map<int, pair<double,int> >::iterator, bool> InsertedElement = AdaptiveCriteriaList->insert( make_pair(*((*marker).second.begin()), pair<double,int>( fabs(Value), FragOrder) ));
    map<int, pair<double,int> >::iterator PresentItem = InsertedElement.first;
    if (!InsertedElement.second) { // this root is already present
      if ((*PresentItem).second.second < FragOrder)  // if order there is lower, update entry with higher-order term
        //if ((*PresentItem).second.first < (*runner).first)    // as higher-order terms are not always better, we skip this part (which would always include this site into adaptive increase)
        {  // if value is smaller, update value and order
        (*PresentItem).second.first = fabs(Value);
        (*PresentItem).second.second = FragOrder;
        DoLog(2) && (Log() << Verbose(2) << "Updated element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl);
      } else {
        DoLog(2) && (Log() << Verbose(2) << "Did not update element " <<  (*PresentItem).first << " as " << FragOrder << " is less than or equal to " << (*PresentItem).second.second << "." << endl);
      }
    } else {
      DoLog(2) && (Log() << Verbose(2) << "Inserted element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl);
    }
  } else {
    DoLog(1) && (Log() << Verbose(1) << "No Fragment under No. " << No << "found." << endl);
  }
};

/** Counts lines in file.
 * Note we are scanning lines from current position, not from beginning.
 * \param InputFile file to be scanned.
 */
int CountLinesinFile(std::ifstream &InputFile)
{
  char *buffer = new char[MAXSTRINGSIZE];
  int lines=0;

  int PositionMarker = InputFile.tellg();  // not needed as Inputfile is copied, given by value, not by ref
  // count the number of lines, i.e. the number of fragments
  InputFile.getline(buffer, MAXSTRINGSIZE); // skip comment lines
  InputFile.getline(buffer, MAXSTRINGSIZE);
  while(!InputFile.eof()) {
    InputFile.getline(buffer, MAXSTRINGSIZE);
    lines++;
  }
  InputFile.seekg(PositionMarker, ios::beg);
  delete[](buffer);
  return lines;
};


/** Scans the adaptive order file and insert (index, value) into map.
 * \param &path path to ENERGYPERFRAGMENT file (may be NULL if Order is non-negative)
 * \param &IndexedKeySetList list to find key set for a given index \a No
 * \return adaptive criteria list from file
 */
std::map<int, std::pair<double,int> > * ScanAdaptiveFileIntoMap(std::string &path, std::map<int,KeySet> &IndexKeySetList)
{
  map<int, pair<double,int> > *AdaptiveCriteriaList = new map<int, pair<double,int> >;
  int No = 0, FragOrder = 0;
  double Value = 0.;
  char buffer[MAXSTRINGSIZE];
  string filename = path + ENERGYPERFRAGMENT;
  ifstream InputFile(filename.c_str());

  if (InputFile.fail()) {
    DoeLog(1) && (eLog() << Verbose(1) << "Cannot find file " << filename << "." << endl);
    return AdaptiveCriteriaList;
  }

  if (CountLinesinFile(InputFile) > 0) {
    // each line represents a fragment root (Atom::Nr) id and its energy contribution
    InputFile.getline(buffer, MAXSTRINGSIZE); // skip comment lines
    InputFile.getline(buffer, MAXSTRINGSIZE);
    while(!InputFile.eof()) {
      InputFile.getline(buffer, MAXSTRINGSIZE);
      if (strlen(buffer) > 2) {
        //Log() << Verbose(2) << "Scanning: " << buffer << endl;
        stringstream line(buffer);
        line >> FragOrder;
        line >> ws >> No;
        line >> ws >> Value; // skip time entry
        line >> ws >> Value;
        No -= 1;  // indices start at 1 in file, not 0
        //Log() << Verbose(2) << " - yields (" << No << "," << Value << ", " << FragOrder << ")" << endl;

        // clean the list of those entries that have been superceded by higher order terms already
        InsertIntoAdaptiveCriteriaList(AdaptiveCriteriaList, IndexKeySetList, FragOrder, No, Value);
      }
    }
    // close and done
    InputFile.close();
    InputFile.clear();
  }

  return AdaptiveCriteriaList;
};

/** Maps adaptive criteria list back onto (Value, (Root Nr., Order))
 * (i.e. sorted by value to pick the highest ones)
 * \param *out output stream for debugging
 * \param &AdaptiveCriteriaList list to insert into
 * \param *mol molecule with atoms
 * \return remapped list
 */
std::map<double, std::pair<int,int> >  * ReMapAdaptiveCriteriaListToValue(std::map<int, std::pair<double,int> > *AdaptiveCriteriaList, molecule *mol)
{
  atom *Walker = NULL;
  map<double, pair<int,int> > *FinalRootCandidates = new map<double, pair<int,int> > ;
  DoLog(1) && (Log() << Verbose(1) << "Root candidate list is: " << endl);
  for(map<int, pair<double,int> >::iterator runner = AdaptiveCriteriaList->begin(); runner != AdaptiveCriteriaList->end(); runner++) {
    Walker = mol->FindAtom((*runner).first);
    if (Walker != NULL) {
      //if ((*runner).second.second >= Walker->AdaptiveOrder) { // only insert if this is an "active" root site for the current order
      if (!Walker->MaxOrder) {
        DoLog(2) && (Log() << Verbose(2) << "(" << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "])" << endl);
        FinalRootCandidates->insert( make_pair( (*runner).second.first, pair<int,int>((*runner).first, (*runner).second.second) ) );
      } else {
        DoLog(2) && (Log() << Verbose(2) << "Excluding (" << *Walker << ", " << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "]), as it has reached its maximum order." << endl);
      }
    } else {
      DoeLog(0) && (eLog()<< Verbose(0) << "Atom No. " << (*runner).second.first << " was not found in this molecule." << endl);
      performCriticalExit();
    }
  }
  return FinalRootCandidates;
};

/** 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);
};