source: src/Filling/Filler.cpp@ 4fbc4eb

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2012 University of Bonn. All rights reserved.
 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
 */

/*
 * Filler.cpp
 *
 *  Created on: Jan 16, 2012
 *      Author: heber
 */


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

#include "CodePatterns/MemDebug.hpp"

#include <algorithm>
#include <boost/bind.hpp>
#include <boost/lambda/lambda.hpp>
#include <sstream>
#include <vector>

#include "Filler.hpp"

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

#include "Atom/atom.hpp"
#include "Box.hpp"
#include "ClusterInterface.hpp"
#include "Descriptors/AtomIdDescriptor.hpp"
#include "Inserter/Inserter.hpp"
#include "LinearAlgebra/RealSpaceMatrix.hpp"
#include "LinearAlgebra/Vector.hpp"
#include "NodeTypes.hpp"
#include "Predicates/FillPredicate.hpp"
#include "Predicates/Ops_FillPredicate.hpp"
#include "World.hpp"


/** Constructor for class Filler.
 *
 * \note We store inverted \a _predicate because we need it only for
 * remove_copy_if which works in this inverted way as desired.
 *
 * @param _mesh Mesh with a NodeSet that fills its Shape
 * @param _predicate predicate construct to check at each Node
 * @param _inserter inserter which places the cloned cluster
 */
Filler::Filler(const Mesh &_mesh, const FillPredicate &_predicate, const Inserter &_inserter) :
  mesh(_mesh),
  predicate(!_predicate),
  inserter(_inserter)
{}

/** Destructor for class Filler.
 *
 */
Filler::~Filler()
{}

/** Fill in the desired Cluster at each remaining node.
 *
 * \note The cluster is non-const because it is moved to the first vacant node.
 *
 * @param copyMethod functor that knows how to copy atoms.
 * @param cluster set of atomic ids contained in a specific Shape to fill each Node with
 * @return true - at least one node has been filled, false - no node filled
 */
bool Filler::operator()(
    CopyAtomsInterface &copyMethod,
    ClusterInterface::Cluster_impl cluster) const
{
  const NodeSet &nodes = mesh.getNodes();
  std::stringstream output;
  std::for_each( nodes.begin(), nodes.end(), output << boost::lambda::_1 << " ");
  LOG(3, "DEBUG: Listing nodes to check: " << output.str());
  if (nodes.size() == 0)
    return false;
  NodeSet FillNodes(nodes.size(), zeroVec);

  // move filler cluster's atoms out of domain such that it does not disturb the predicate.
  // we only move the atoms as otherwise two translate ShapeOps will be on top of the Shape
  // which is subsequently copied to all other cloned Clusters ...
  Vector BoxDiagonal;
  {
    const RealSpaceMatrix &M = World::getInstance().getDomain().getM();
    BoxDiagonal = (M * Vector(1.,1.,1.));
    BoxDiagonal -= cluster->getShape().getCenter();
    BoxDiagonal *= 1. + 2.*cluster->getShape().getRadius()/BoxDiagonal.Norm(); // extend it a little further
    AtomIdSet atoms = cluster->getAtoms();
    for (AtomIdSet::iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
      (*iter)->setPosition( (*iter)->getPosition() + BoxDiagonal );
    LOG(1, "INFO: Translating original cluster's atoms by " << BoxDiagonal << ".");
  }

  // evaluate predicate and gather into new set
  NodeSet::iterator transform_end  =
      std::remove_copy_if(nodes.begin(), nodes.end(), FillNodes.begin(), predicate );
  FillNodes.erase(transform_end, FillNodes.end());

  // shift cluster back to original place
  {
    AtomIdSet atoms = cluster->getAtoms();
    for (AtomIdSet::iterator iter = atoms.begin(); iter != atoms.end(); ++iter)
      (*iter)->setPosition( (*iter)->getPosition() - BoxDiagonal );
    LOG(1, "INFO: Translating original cluster's atoms back.");
  }

  if (FillNodes.size() == 0) {
    ELOG(2, "For none of the nodes did the predicate return true.");
    return false;
  } else {
    LOG(1, "INFO: " << FillNodes.size() << " out of " << nodes.size() << " returned true from predicate.");
  }

  // clone clusters
  std::vector<ClusterInterface::Cluster_impl> clusters(FillNodes.size());
  std::vector<ClusterInterface::Cluster_impl>::iterator clusteriter = clusters.begin();
  *clusteriter = cluster;
  clusteriter++;
  std::generate_n(clusteriter, FillNodes.size()-1,
      boost::bind(&ClusterInterface::clone, boost::cref(cluster), boost::ref(copyMethod), zeroVec) );

  // insert each cluster by abusing std::search a bit:
  // we look for the subsequence of FillNodes inside clusters. If Inserter always
  // returns true, we'll have the iterator pointing at first cluster
  std::vector<ClusterInterface::Cluster_impl>::const_iterator inserteriter =
    std::search(clusters.begin(), clusters.end(), FillNodes.begin(), FillNodes.end(),
        boost::bind(&Inserter::operator(), boost::cref(inserter), _1, _2));
  if( inserteriter != clusters.begin()) {
    ELOG(1, "Not all cloned clusters could be successfully inserted.");
    return false;
  }

  // give final statment on whether at least \a single cluster has been placed
  if ( FillNodes.size() != 0)
    return true;
  else
    return false;
}