source: src/Actions/MoleculeAction/FillWithMoleculeAction.cpp@ a8b10a

/*
 * 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.
 */

/*
 * FillWithMoleculeAction.cpp
 *
 *  Created on: May 10, 2010
 *      Author: heber
 */

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

#include "CodePatterns/MemDebug.hpp"

#include "atom.hpp"
#include "Graph/BondGraph.hpp"
#include "boundary.hpp"
#include "CodePatterns/Verbose.hpp"
#include "config.hpp"
#include "Descriptors/MoleculeIdDescriptor.hpp"
#include "Descriptors/MoleculeOrderDescriptor.hpp"
#include "molecule.hpp"
#include "Parser/FormatParserStorage.hpp"
#include "World.hpp"

#include <iostream>
#include <string>

#include "Actions/MoleculeAction/FillWithMoleculeAction.hpp"

using namespace MoleCuilder;

// and construct the stuff
#include "FillWithMoleculeAction.def"
#include "Action_impl_pre.hpp"
/** =========== define the function ====================== */
Action::state_ptr MoleculeFillWithMoleculeAction::performCall() {

  // obtain information
  getParametersfromValueStorage();

  DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, "
      << " minimum distance to molecules" << params.boundary
      << ", random atom displacement " << params.RandAtomDisplacement
      << ", random molecule displacement " << params.RandMoleculeDisplacement
      << ", distances between fillers (" << params.distances[0] << "," << params.distances[1] << "," << params.distances[2]
      << "), MinDistance " << params.MaxDistance
      << ", DoRotate " << params.DoRotate << "." << endl);
  // construct water molecule
  std::vector<molecule *> presentmolecules = World::getInstance().getAllMolecules();
//  DoLog(0) && (Log() << Verbose(0) << presentmolecules.size() << " molecules initially are present." << std::endl);
  std::string FilenameSuffix = params.fillername.string().substr(params.fillername.string().find_last_of('.')+1, params.fillername.string().length());
  ifstream input;
  input.open(params.fillername.string().c_str());
  ParserTypes type = FormatParserStorage::getInstance().getTypeFromSuffix(FilenameSuffix);
  FormatParser &parser = FormatParserStorage::getInstance().get(type);
  parser.load(&input);

  // search the filler molecule that has been just parsed
  molecule *filler = World::getInstance().getMolecule(MoleculeByOrder(-1)); // get last molecule
  filler->SetNameFromFilename(params.fillername.string().c_str());
  molecule *Filling = NULL;
//    atom *first = NULL, *second = NULL, *third = NULL;
//    first = World::getInstance().createAtom();
//    first->type = World::getInstance().getPeriode()->FindElement(1);
//    first->x = Vector(0.441, -0.143, 0.);
//    filler->AddAtom(first);
//    second = World::getInstance().createAtom();
//    second->type = World::getInstance().getPeriode()->FindElement(1);
//    second->x = Vector(-0.464, 1.137, 0.0);
//    filler->AddAtom(second);
//    third = World::getInstance().createAtom();
//    third->type = World::getInstance().getPeriode()->FindElement(8);
//    third->x = Vector(-0.464, 0.177, 0.);
//    filler->AddAtom(third);
//    filler->AddBond(first, third, 1);
//    filler->AddBond(second, third, 1);
  molecule::atomVector Set = filler->getAtomSet();
  World::getInstance().getBondGraph()->CreateAdjacency(Set);
//    filler->SetNameFromFilename("water");
  // TODO: Remove the erasure of molecule when saving does not depend on them anymore.
  World::getInstance().getMolecules()->erase(filler); // remove it, Parser adds it automatically

  // call routine
  double distance[NDIM];
  for (int i=0;i<NDIM;i++)
    distance[i] = params.distances[i];
  FillBoxWithMolecule(
      World::getInstance().getMolecules(),
      filler, *(World::getInstance().getConfig()),
      params.MaxDistance,
      distance,
      params.boundary,
      params.RandAtomDisplacement,
      params.RandMoleculeDisplacement,
      params.DoRotate);
  for (molecule::iterator iter = filler->begin(); !filler->empty(); iter = filler->begin()) {
    atom *Walker = *iter;
    World::getInstance().destroyAtom(Walker);
  }
  World::getInstance().destroyMolecule(filler);

  // generate list of newly created molecules
  // (we can in general remove more quickly from a list than a vector)
  std::vector<molecule *> fillermolecules = World::getInstance().getAllMolecules();
//  DoLog(0) && (Log() << Verbose(0) << fillermolecules.size() << " molecules are present." << std::endl);
  std::list<molecule *> fillermolecules_list;
  std::copy( fillermolecules.begin(),  fillermolecules.end(), std::back_inserter( fillermolecules_list ));
//  DoLog(0) && (Log() << Verbose(0) << fillermolecules_list.size() << " molecules have been copied." << std::endl);
  for (std::vector<molecule *>::const_iterator iter = presentmolecules.begin();
      iter != presentmolecules.end();
      ++iter) {
    fillermolecules_list.remove(*iter);
  }
//  DoLog(0) && (Log() << Verbose(0) << fillermolecules_list.size() << " molecules left after removal." << std::endl);
  fillermolecules.clear();
  std::copy(fillermolecules_list.begin(), fillermolecules_list.end(), std::back_inserter( fillermolecules ));

//  DoLog(0) && (Log() << Verbose(0) << fillermolecules.size() << " molecules have been inserted." << std::endl);

  return Action::state_ptr(new MoleculeFillWithMoleculeState(fillermolecules,params));
}

Action::state_ptr MoleculeFillWithMoleculeAction::performUndo(Action::state_ptr _state) {
  MoleculeFillWithMoleculeState *state = assert_cast<MoleculeFillWithMoleculeState*>(_state.get());

  MoleculeListClass *MolList = World::getInstance().getMolecules();

  BOOST_FOREACH(molecule *_mol, state->fillermolecules) {
    MolList->erase(_mol);
    if ((_mol != NULL) && (!(World::getInstance().getAllMolecules(MoleculeById(_mol->getId()))).empty())) {
      for(molecule::iterator iter = _mol->begin();
          !_mol->empty();
          iter = _mol->begin()) {
        atom *Walker = *iter;
        World::getInstance().destroyAtom(Walker);
      }
      World::getInstance().destroyMolecule(_mol);
    }
  }

  // as molecules and atoms from state are removed, we have to create a new one
  std::vector<molecule *> fillermolecules;
  return Action::state_ptr(new MoleculeFillWithMoleculeState(fillermolecules,state->params));
}

Action::state_ptr MoleculeFillWithMoleculeAction::performRedo(Action::state_ptr _state){
  //MoleculeFillWithMoleculeState *state = assert_cast<MoleculeFillWithMoleculeState*>(_state.get());

  return Action::failure;
  //return Action::state_ptr(_state);
}

bool MoleculeFillWithMoleculeAction::canUndo() {
  return true;
}

bool MoleculeFillWithMoleculeAction::shouldUndo() {
  return true;
}
/** =========== end of function ====================== */