source: src/Filling/Inserter/SurfaceInserter.cpp@ c4f43e

/*
 * 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.
 */

/*
 * SurfaceInserter.cpp
 *
 *  Created on: Apr 03, 2012
 *      Author: heber
 */


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

#include "CodePatterns/MemDebug.hpp"

#include "SurfaceInserter.hpp"

#include "Atom/atom.hpp"
#include "CodePatterns/Log.hpp"
#include "LinearAlgebra/RealSpaceMatrix.hpp"
#include "LinearAlgebra/Vector.hpp"
#include "Shapes/Shape.hpp"

/** Constructor for class SurfaceInserter.
 *
 * @param _s shape on whose surface the insertion nodes lie
 * @param _alignedAxis axis along which to be inserted cluster is aligned to
 */
SurfaceInserter::SurfaceInserter(const Shape & _s, const Vector &_alignedAxis) :
    shape(_s),
    alignedAxis(_alignedAxis)
{}

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

/** Inserter operator that rotates the cluster to be perpendicular on surface at
 *  desired \a offset and translates it there.
 *
 * \note We assume that cluster is aligned along \a SurfaceInserter::alignedAxis and
 * the translation is done relative to origin.
 *
 * @param offset
 * @return always true
 */
bool SurfaceInserter::operator()(ClusterInterface::Cluster_impl cluster, const Vector &offset) const
{
  // create rotation matrix, assuming cluster is aligned along z axis
  Vector SurfaceNormal = shape.getNormal(offset); // get normal at desired point
  LOG(3, "DEBUG: Normal vector at " << offset << " is " << SurfaceNormal << ".");
  const double alpha = - alignedAxis.Angle(SurfaceNormal); // we have to rotate back
  LOG(4, "DEBUG: Rotation angle is " << alpha << ".");
  SurfaceNormal.VectorProduct(alignedAxis);  // get the rotation axis as normal direction to both
  SurfaceNormal.Normalize();
  LOG(4, "DEBUG: Rotation axis is " << SurfaceNormal << ".");
  RealSpaceMatrix M;
  M.setRotation(SurfaceNormal, alpha);

  // rotate cluster
  cluster->transform(M);

  // translate
  cluster->translate(offset);

  return true;
}