xyzwriter.h

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/*
 * Copyright 2009-2021 The VOTCA Development Team (http://www.votca.org)
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */
 
#ifndef VOTCA_CSG_XYZWRITER_H
#define VOTCA_CSG_XYZWRITER_H
 
// Standard includes
#include <cstdio>
 
// VOTCA includes
#include <votca/tools/constants.h>
#include <votca/tools/unitconverter.h>
 
// Local VOTCA includes
#include "topology.h"
#include "trajectorywriter.h"
 
namespace votca {
namespace csg {
 
class XYZWriter : public TrajectoryWriter {
 public:
  const tools::DistanceUnit distance_unit = tools::DistanceUnit::angstroms;
 
  void Open(std::string file, bool bAppend = false) override;
  void Close() override;
 
  void Write(Topology *conf) override;
 
  template <class T>
  void Write(T &container, std::string header);
 
 private:
  template <class T>
  Index getSize(T &container) {
    return getIterable(container).size();
  }
 
  template <class Atom>
  std::string getName(Atom &atom) {
    return atom.getElement();
  }
 
  std::string getName(std::unique_ptr<Bead> &bead) { return bead->getName(); }
 
  template <class Atom>
  Eigen::Vector3d getPos(Atom &atom) {
    return atom.getPos() * tools::conv::bohr2ang;
  }
 
  Eigen::Vector3d getPos(std::unique_ptr<Bead> &bead) {
    return bead->Pos() * tools::conv::nm2ang;
  }
 
  template <class T>
  T &getIterable(T &container) {
    return container;
  }
 
  BeadContainer &getIterable(Topology &top) { return top.Beads(); }
 
  std::ofstream out_;
};
 
template <class T>
inline void XYZWriter::Write(T &container, std::string header) {
  out_ << getSize(container) << "\n";
  out_ << header << "\n";
 
  boost::format fmter("%1$s%2$10.5f%3$10.5f%4$10.5f\n");
 
  for (auto &atom : getIterable(container)) {
    Eigen::Vector3d r = getPos(atom);
    // truncate strings if necessary
    std::string atomname = getName(atom);
    if (atomname.size() > 3) {
      atomname = atomname.substr(0, 3);
    }
    while (atomname.size() < 3) {
      atomname = " " + atomname;
    }
 
    out_ << fmter % atomname % r.x() % r.y() % r.z();
  }
  out_ << std::flush;
}
}  // namespace csg
}  // namespace votca
 
#endif  // VOTCA_CSG_XYZWRITER_H