beadstructure.h

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/*
 * Copyright 2009-2019 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_CSG_BEADSTRUCTURE_H
#define VOTCA_CSG_BEADSTRUCTURE_H
 
// Standard inlcudes
#include <unordered_map>
 
// VOTCA includes
#include <votca/tools/graph.h>
 
namespace votca {
namespace csg {
 
class BeadStructure {
 public:
  virtual ~BeadStructure() = default;
 
  BeadStructure getSubStructure(const std::vector<Index> &idx,
                                const std::vector<tools::Edge> &edges) const;
 
  bool isSingleStructure();
 
  size_t BeadCount() const noexcept { return beads_.size(); }
 
  template <class T>
  void AddBead(const T &bead);
 
  virtual void ConnectBeads(const Index &bead1_id, const Index &bead2_id);
 
  std::vector<Index> getNeighBeadIds(const Index &index);
 
  tools::Graph getGraph();
 
  bool isStructureEquivalent(BeadStructure &beadstructure);
 
  bool BeadExist(Index bead_id) const { return beads_.count(bead_id); }
 
  std::vector<Index> getBeadIds() const;
 
 protected:
  struct BeadInfo {
    double mass = 0.0;
    std::string name = "";
  };
  virtual void UpdateOnBeadAddition_() {};
  void InitializeGraph_();
  void CalculateStructure_();
  tools::GraphNode BeadInfoToGraphNode_(const BeadInfo &);
 
  bool structureIdUpToDate = false;
  bool graphUpToDate = false;
  bool single_structureUpToDate_ = false;
  bool single_structure_ = false;
  std::string structure_id_ = "";
  tools::Graph graph_;
  std::set<tools::Edge> connections_;
  std::unordered_map<Index, BeadInfo> beads_;
  std::unordered_map<Index, tools::GraphNode> graphnodes_;
};
 
template <class T>
void BeadStructure::AddBead(const T &bead) {
  if (beads_.count(bead.getId())) {
    std::string err = "Cannot add bead with Id ";
    err += std::to_string(bead.getId());
    err += " because each bead must have a unique Id and a bead with that Id ";
    err += "already exists within the beadstructure";
    throw std::invalid_argument(err);
  }
  UpdateOnBeadAddition_();
  size_t numberOfBeads = beads_.size();
  BeadInfo bead_info;
  bead_info.mass = bead.getMass();
  bead_info.name = bead.getName();
 
  beads_[bead.getId()] = bead_info;
 
  if (numberOfBeads != beads_.size()) {
    single_structureUpToDate_ = false;
    graphUpToDate = false;
    structureIdUpToDate = false;
  }
}
 
}  // namespace csg
}  // namespace votca
 
#endif  // VOTCA_CSG_BEADSTRUCTURE_H