jobtopology.h

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/*
 *            Copyright 2009-2020 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.
 *
 */
 
#pragma once
#ifndef VOTCA_XTP_JOBTOPOLOGY_H
#define VOTCA_XTP_JOBTOPOLOGY_H
 
// Local VOTCA includes
#include "job.h"
#include "logger.h"
#include "region.h"
#include "topology.h"
 
namespace votca {
namespace xtp {
class SegId;
class JobTopology {
 public:
  JobTopology(Job& job, Logger& log, std::string workdir)
      : job_(job), log_(log), workdir_(workdir) {};
  void BuildRegions(const Topology& top,
                    std::pair<std::string, tools::Property> options);
 
  void WriteToHdf5(std::string filename) const;
 
  void ReadFromHdf5(std::string filename);
 
  void WriteToPdb(std::string filename) const;
 
  std::vector<std::unique_ptr<Region> >::iterator begin() {
    return regions_.begin();
  }
  std::vector<std::unique_ptr<Region> >::iterator end() {
    return regions_.end();
  }
 
  const std::vector<std::unique_ptr<Region> >& Regions() const {
    return regions_;
  }
 
  std::vector<std::unique_ptr<Region> >& Regions() { return regions_; }
 
  Index size() const { return Index(regions_.size()); }
 
  std::vector<std::unique_ptr<Region> >::const_iterator begin() const {
    return regions_.begin();
  }
  std::vector<std::unique_ptr<Region> >::const_iterator end() const {
    return regions_.end();
  }
 
 private:
  std::vector<std::vector<SegId> > PartitionRegions(
      const tools::Property& regions_def, const Topology& top) const;
 
  void CreateRegions(const std::pair<std::string, tools::Property>& options,
                     const Topology& top,
                     const std::vector<std::vector<SegId> >& region_seg_ids);
 
  void ModifyOptionsByJobFile(tools::Property& regions_def) const;
 
  template <class T>
  void ShiftPBC(const Topology& top, const Eigen::Vector3d& center,
                T& mol) const;
 
  void CheckEnumerationOfRegions(const tools::Property& regions_def) const;
  std::vector<const tools::Property*> SortRegionsDefbyId(
      const tools::Property& regions_def) const;
 
  Job& job_;
  Logger& log_;
  std::vector<std::unique_ptr<Region> > regions_;
  std::string workdir_ = "";
 
  static constexpr int jobtopology_version() { return 1; }
};
}  // namespace xtp
}  // namespace votca
 
#endif  // VOTCA_XTP_JOBTOPOLOGY_H