source: src/Actions/WorldAction/RepeatBoxAction.cpp@ 5fd0f4

/*
 * 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.
 */

/*
 * RepeatBoxAction.cpp
 *
 *  Created on: May 12, 2010
 *      Author: heber
 */

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

#include "CodePatterns/MemDebug.hpp"

#include "Descriptors/MoleculePtrDescriptor.hpp"
#include "atom.hpp"
#include "CodePatterns/Log.hpp"
#include "molecule.hpp"
#include "LinearAlgebra/Vector.hpp"
#include "LinearAlgebra/RealSpaceMatrix.hpp"
#include "CodePatterns/Verbose.hpp"
#include "World.hpp"
#include "Box.hpp"

#include <iostream>
#include <set>
#include <string>
#include <vector>

#include "Actions/WorldAction/RepeatBoxAction.hpp"

using namespace MoleCuilder;

// and construct the stuff
#include "RepeatBoxAction.def"
#include "Action_impl_pre.hpp"
/** =========== define the function ====================== */

void repeatMoleculesinDomain(Vector Repeater, const std::vector<molecule *> &AllMolecules)
{
  int count;
  const element ** Elements;
  int j = 0;
  atom *Walker = NULL;
  MoleculeListClass *molecules = World::getInstance().getMolecules();

  LOG(0, "STATUS: Repeating box " << Repeater << " times for (x,y,z) axis.");

  // set new domain
  RealSpaceMatrix M = World::getInstance().getDomain().getM();
  RealSpaceMatrix newM = M;
  Vector x,y;
  int n[NDIM];
  RealSpaceMatrix repMat;
  for (int axis = 0; axis < NDIM; axis++) {
    Repeater[axis] = floor(Repeater[axis]);
    if (Repeater[axis] < 1) {
      ELOG(1, "Repetition factor must be greater than 1!");
      Repeater[axis] = 1;
    }
    repMat.at(axis,axis) = Repeater[axis];
  }
  newM *= repMat;
  World::getInstance().setDomain(newM);

  // add molecules in each repeated domain part
  molecule *newmol = NULL;
  std::vector<Vector> vectors;
  for (n[0] = 0; n[0] < Repeater[0]; n[0]++) {
    y[0] = n[0];
    for (n[1] = 0; n[1] < Repeater[1]; n[1]++) {
      y[1] = n[1];
      for (n[2] = 0; n[2] < Repeater[2]; n[2]++) {
        y[2] = n[2];
        if ((n[0] == 0) && (n[1] == 0) && (n[2] == 0))
          continue;
        for (vector<molecule *>::const_iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
          const molecule *mol = *MolRunner;
          LOG(2, "INFO: Current mol is " << mol->name << ".");
          count = mol->getAtomCount();   // is changed becausing of adding, thus has to be stored away beforehand
          if (count != 0) {  // if there is more than none
            Elements = new const element *[count];
            vectors.resize(count);
            j = 0;
            for(molecule::const_iterator AtomRunner = mol->begin(); AtomRunner != mol->end(); ++AtomRunner) {
              Elements[j] = (*AtomRunner)->getType();
              vectors[j] = (*AtomRunner)->getPosition();
              j++;
            }
            if (count != j)
              ELOG(1, "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!");
            x = y;
            x *= M;
            newmol = World::getInstance().createMolecule();
            // TODO: Remove this when World don't has deprecated MoleculeListClass anymore
            molecules->insert(newmol);
            for (int k=count;k--;) { // go through every atom of the original cell
              Walker = World::getInstance().createAtom(); // create a new body
              Walker->setPosition((vectors[k]) + x);
              Walker->setType(Elements[k]);  // insert original element
              cout << "new atom is " << *Walker << endl;
              newmol->AddAtom(Walker);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
            }
            // free memory
            delete[](Elements);
          } else {
            LOG(1, "\t ... is empty.");
          }
        }
      }
    }
  }
}

Action::state_ptr WorldRepeatBoxAction::performCall() {
  molecule *mol = NULL;

  // obtain information
  getParametersfromValueStorage();

  std::vector<molecule *> AllMolecules;
  if (mol != NULL) {
    DoLog(0) && (Log() << Verbose(0) << "Using molecule " << mol->name << "." << endl);
    AllMolecules = World::getInstance().getAllMolecules(MoleculeByPtr(mol));
  } else {
    DoLog(0) && (Log() << Verbose(0) << "Using all molecules." << endl);
    AllMolecules = World::getInstance().getAllMolecules();
  }

  // prepare undo state
  RealSpaceMatrix olddomain = World::getInstance().getDomain().getM();
  std::set<molecule *> oldmolecules;
  for(std::vector<molecule *>::const_iterator iter = AllMolecules.begin();
      iter != AllMolecules.end();
      ++iter)
    oldmolecules.insert(*iter);
  WorldRepeatBoxState *undostate = new WorldRepeatBoxState(olddomain, oldmolecules, params);

  repeatMoleculesinDomain(params.Repeater, AllMolecules);

  // give final box size
  LOG(0, "Box domain is now " << World::getInstance().getDomain().getM());

  return Action::state_ptr(undostate);
}

Action::state_ptr WorldRepeatBoxAction::performUndo(Action::state_ptr _state) {
  WorldRepeatBoxState *state = assert_cast<WorldRepeatBoxState*>(_state.get());
  MoleculeListClass *molecules = World::getInstance().getMolecules();

  // set old domain
  World::getInstance().setDomain(state->olddomain);

  // remove all added molecules (and their atoms)
  std::vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
  for (std::vector<molecule *>::iterator iter = allmolecules.begin();
      iter != allmolecules.end();
      ++iter) {
    if (state->oldmolecules.find(*iter) == state->oldmolecules.end()) {
      (*iter)->removeAtomsinMolecule();
      // TODO: Remove this when World don't has deprecated MoleculeListClass anymore
      molecules->erase(*iter);
      World::getInstance().destroyMolecule(*iter);
    }
  }

  // give final box size
  LOG(0, "Box domain restored to " << World::getInstance().getDomain().getM());

  return Action::state_ptr(_state);
}

Action::state_ptr WorldRepeatBoxAction::performRedo(Action::state_ptr _state){
  WorldRepeatBoxState *state = assert_cast<WorldRepeatBoxState*>(_state.get());

  std::vector<molecule *> originalmolecules;
  for(std::set<molecule *>::const_iterator iter = state->oldmolecules.begin();
      iter != state->oldmolecules.end();
      ++iter)
    originalmolecules.push_back(*iter);
  repeatMoleculesinDomain(state->params.Repeater, originalmolecules);

  // give final box size
  LOG(0, "Box domain is again " << World::getInstance().getDomain().getM());

  return Action::state_ptr(_state);
}

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

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