source: src/Actions/MoleculeAction/StretchBondAction.cpp@ 4464ef

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2012 University of Bonn. All rights reserved.
 * 
 *
 *   This file is part of MoleCuilder.
 *
 *    MoleCuilder is free software: you can redistribute it and/or modify
 *    it under the terms of the GNU General Public License as published by
 *    the Free Software Foundation, either version 2 of the License, or
 *    (at your option) any later version.
 *
 *    MoleCuilder is distributed in the hope that it will be useful,
 *    but WITHOUT ANY WARRANTY; without even the implied warranty of
 *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *    GNU General Public License for more details.
 *
 *    You should have received a copy of the GNU General Public License
 *    along with MoleCuilder.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 * StretchBondAction.cpp
 *
 *  Created on: Sep 26, 2012
 *      Author: heber
 */

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

#include "CodePatterns/MemDebug.hpp"

#include "Actions/MoleculeAction/StretchBondAction.hpp"

#include "CodePatterns/Log.hpp"
#include "CodePatterns/Verbose.hpp"

#include "LinearAlgebra/Plane.hpp"

#include "Atom/atom.hpp"
#include "Bond/bond.hpp"
#include "molecule.hpp"
#include "World.hpp"

using namespace MoleCuilder;

// and construct the stuff
#include "StretchBondAction.def"
#include "Action_impl_pre.hpp"
/** =========== define the function ====================== */
ActionState::ptr MoleculeStretchBondAction::performCall()
{
  // check preconditions
  const std::vector< atom *> atoms = World::getInstance().getSelectedAtoms();
  if (atoms.size() != 2) {
    STATUS("Exactly two atoms must be selected.");
    return Action::failure;
  }
  molecule *mol = World::getInstance().
      getMolecule(MoleculeById(atoms[0]->getMolecule()->getId()));
  if (mol != atoms[1]->getMolecule()) {
    STATUS("The two selected atoms must belong to the same molecule.");
    return Action::failure;
  }
  // gather undo information
  const double olddistance = atoms[0]->getPosition().distance(atoms[1]->getPosition());
  const double newdistance = params.bonddistance.get();
  LOG(1, "INFO: Old bond distance is " << olddistance << ", stretching to " << newdistance << ".");

  // create the bond plane and mid-distance
  const Vector NormalVector = (atoms[0]->getPosition() - atoms[1]->getPosition())* (1./olddistance);
  const Vector OffsetVector = 0.5*(atoms[0]->getPosition() + atoms[1]->getPosition());
  Plane bondplane(NormalVector, OffsetVector);
  // go through the molecule and stretch each atom relative two plane
  const double shift = 0.5*(newdistance - olddistance);
  const Vector PositiveShift = shift * NormalVector;
  const Vector NegativeShift = -shift * NormalVector;
  Box &domain = World::getInstance().getDomain();
  for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
    const Vector &position = (*iter)->getPosition();
    // for each atom determine on which side of plane it is and shift accordingly
    if (bondplane.SignedDistance(position) > 0) {
      (*iter)->setPosition( domain.enforceBoundaryConditions(position+PositiveShift) );
    } else {
      (*iter)->setPosition( domain.enforceBoundaryConditions(position+NegativeShift) );
    }
  }

  MoleculeStretchBondState *UndoState = new MoleculeStretchBondState(shift, bondplane, mol, params);
  return ActionState::ptr(UndoState);
}

ActionState::ptr MoleculeStretchBondAction::performUndo(ActionState::ptr _state) {
  MoleculeStretchBondState *state = assert_cast<MoleculeStretchBondState*>(_state.get());

  // use given plane to undo
  const Vector PositiveShift = state->shift * state->bondplane.getNormal();
  const Vector NegativeShift = -state->shift * state->bondplane.getNormal();
  Box &domain = World::getInstance().getDomain();
  molecule *mol = World::getInstance().
      getMolecule(MoleculeById(state->mol->getId()));
  for (molecule::iterator iter = mol->begin();
      iter != mol->end(); ++iter) {
    const Vector &position = (*iter)->getPosition();
    // for each atom determine on which side of plane it is and shift accordingly
    if (state->bondplane.SignedDistance(position) < 0) {
      (*iter)->setPosition( domain.enforceBoundaryConditions(position+PositiveShift) );
    } else {
      (*iter)->setPosition( domain.enforceBoundaryConditions(position+NegativeShift) );
    }
  }

  return ActionState::ptr(_state);
}

ActionState::ptr MoleculeStretchBondAction::performRedo(ActionState::ptr _state){
  MoleculeStretchBondState *state = assert_cast<MoleculeStretchBondState*>(_state.get());

  // use given plane to undo
  const Vector PositiveShift = state->shift * state->bondplane.getNormal();
  const Vector NegativeShift = -state->shift * state->bondplane.getNormal();
  Box &domain = World::getInstance().getDomain();
  molecule *mol = World::getInstance().
      getMolecule(MoleculeById(state->mol->getId()));
  for (molecule::iterator iter = mol->begin();
      iter != mol->end(); ++iter) {
    const Vector &position = (*iter)->getPosition();
    // for each atom determine on which side of plane it is and shift accordingly
    if (state->bondplane.SignedDistance(position) > 0) {
      (*iter)->setPosition( domain.enforceBoundaryConditions(position+PositiveShift) );
    } else {
      (*iter)->setPosition( domain.enforceBoundaryConditions(position+NegativeShift) );
    }
  }
  return ActionState::ptr(_state);
}

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

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