source: src/Fragmentation/AdaptivityMap.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.
 */

/*
 * AdaptivityMap.cpp
 *
 *  Created on: Oct 20, 2011
 *      Author: heber
 */

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

#include "CodePatterns/MemDebug.hpp"

#include "AdaptivityMap.hpp"

#include <fstream>

#include "CodePatterns/Log.hpp"

#include "atom.hpp"
#include "Helpers/defs.hpp"
#include "Helpers/helpers.hpp"
#include "molecule.hpp"

/** Constructor of class AdaptivityMap.
 *
 */
AdaptivityMap::AdaptivityMap()
{}

/** Destructor of class AdaptivityMap.
 *
 */
AdaptivityMap::~AdaptivityMap()
{}

/** 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 AdaptivityMap::InsertIntoAdaptiveCriteriaList(std::map<int, std::pair<double,int> > *AdaptiveCriteriaList, int FragOrder, int No, double Value) const
{
  const_iterator marker = find(No);    // find keyset to Frag No.
  if (marker != 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
    std::pair <map<int, pair<double,int> >::iterator, bool> InsertedElement = AdaptiveCriteriaList->insert( make_pair(*((*marker).second.begin()), pair<double,int>( fabs(Value), FragOrder) ));
    std::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);
  }
};


/** 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)
 * \return adaptive criteria list from file
 */
std::map<int, std::pair<double,int> > * AdaptivityMap::ScanAdaptiveFileIntoMap(std::string &path)
{
  std::map<int, pair<double,int> > *AdaptiveCriteriaList = new std::map<int, pair<double,int> >;
  int No = 0, FragOrder = 0;
  double Value = 0.;
  char buffer[MAXSTRINGSIZE];
  std::string filename = path + ENERGYPERFRAGMENT;
  std::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, 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> >  * AdaptivityMap::ReMapAdaptiveCriteriaListToValue(std::map<int, std::pair<double,int> > *AdaptiveCriteriaList, molecule *mol)
{
  atom *Walker = NULL;
  std::map<double, std::pair<int,int> > *FinalRootCandidates = new std::map<double, std::pair<int,int> > ;
  DoLog(1) && (Log() << Verbose(1) << "Root candidate list is: " << endl);
  for(std::map<int, std::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;
};

/** Counts lines in file.
 * Note we are scanning lines from current position, not from beginning.
 * \param InputFile file to be scanned.
 */
int AdaptivityMap::CountLinesinFile(std::ifstream &InputFile) const
{
  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;
};