lammpsdatareader.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.
 *
 */
 
#ifndef VOTCA_CSG_LAMMPSDATAREADER_PRIVATE_H
#define VOTCA_CSG_LAMMPSDATAREADER_PRIVATE_H
 
// Standard includes
#include <fstream>
#include <iostream>
#include <string>
 
// VOTCA includes
#include <votca/tools/unitconverter.h>
 
// Local VOTCA includes
#include "votca/csg/topologyreader.h"
#include "votca/csg/trajectoryreader.h"
 
namespace votca {
namespace csg {
 
class Molecule;
 
class LAMMPSDataReader : public TrajectoryReader, public TopologyReader {
 public:
  const tools::DistanceUnit distance_unit = tools::DistanceUnit::angstroms;
  const tools::TimeUnit time_unit = tools::TimeUnit::femtoseconds;
  const tools::MassUnit mass_unit = tools::MassUnit::grams_per_mole;
  const tools::MolarEnergyUnit energy_unit =
      tools::MolarEnergyUnit::kilocalories_per_mole;
  const tools::ChargeUnit charge_unit = tools::ChargeUnit::e;
  const tools::MolarForceUnit force_unit =
      tools::MolarForceUnit::kilocalories_per_mole_angstrom;
 
  LAMMPSDataReader() = default;
  ~LAMMPSDataReader() override = default;
 
  bool ReadTopology(std::string file, Topology &top) override;
 
  bool Open(const std::string &file) override;
  bool FirstFrame(Topology &top) override;
  bool NextFrame(Topology &top) override;
  void Close() override;
 
 private:
  std::ifstream fl_;
  std::string fname_;
  bool topology_;
 
  std::map<std::string, std::vector<std::vector<std::string>>> data_;
 
  // Index - atom type starting index of 0
  // .at(0) - element symbol or bead
  // .at(1) - atom name may be the same as the element symbol or bead depending
  //          on if there is more than one atom type for a given element
  std::map<Index, std::string> atomtypes_;
 
  // String is the type .e.g. "atom","bond" etc
  // Index is the number of different types
  std::map<std::string, Index> numberOfDifferentTypes_;
 
  // String is the type .e.g. "atom", "bond" etc
  // Index is the number of them
  std::map<std::string, Index> numberOf_;
 
  // First Index is the molecule id
  // Second Index is the molecule ptr
  std::map<Index, Molecule *> molecules_;
 
  // First Index is the atom id second the molecule id
  std::map<Index, Index> atomIdToMoleculeId_;
 
  // First Index is the atom id second the atom index
  std::map<Index, Index> atomIdToIndex_;
 
  bool MatchOneFieldLabel_(std::vector<std::string> fields, Topology &top);
  bool MatchTwoFieldLabels_(std::vector<std::string> fields, Topology &top);
  bool MatchThreeFieldLabels_(std::vector<std::string> fields);
  bool MatchFourFieldLabels_(std::vector<std::string> fields, Topology &top);
 
  void ReadBox_(std::vector<std::string> fields, Topology &top);
  void SortIntoDataGroup_(std::string tag);
  void ReadNumTypes_(std::vector<std::string> fields, std::string type);
 
  void ReadNumOfAtoms_(std::vector<std::string> fields, Topology &top);
  void ReadNumOfBonds_(std::vector<std::string> fields);
  void ReadNumOfAngles_(std::vector<std::string> fields);
  void ReadNumOfDihedrals_(std::vector<std::string> fields);
  void ReadNumOfImpropers_(std::vector<std::string> fields);
 
  void ReadAtoms_(Topology &top);
  void ReadBonds_(Topology &top);
  void ReadAngles_(Topology &top);
  void ReadDihedrals_(Topology &top);
  void SkipImpropers_();
 
  void RenameMolecules(MoleculeContainer &molecules) const;
 
  enum lammps_format {
    style_angle_bond_molecule = 0,
    style_atomic = 1,
    style_full = 2
  };
  lammps_format determineDataFileFormat_(std::string line);
 
  void InitializeAtomAndBeadTypes_();
};
}  // namespace csg
}  // namespace votca
 
#endif  // VOTCA_CSG_LAMMPSDATAREADER_PRIVATE_H