h5md_core.hpp

Go to the documentation of this file.

/*
 * Copyright (C) 2010-2022 The ESPResSo project
 * Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
 *   Max-Planck-Institute for Polymer Research, Theory Group
 *
 * This file is part of ESPResSo.
 *
 * ESPResSo is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * ESPResSo is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
#ifndef CORE_IO_WRITER_H5MD_CORE_HPP
#define CORE_IO_WRITER_H5MD_CORE_HPP
 
#include "BoxGeometry.hpp"
#include "ParticleRange.hpp"
#include "h5md_specification.hpp"
 
#include <utils/Vector.hpp>
 
#include <boost/filesystem.hpp>
#include <boost/mpi/communicator.hpp>
 
#include <h5xx/h5xx.hpp>
 
#include <cstddef>
#include <stdexcept>
#include <string>
#include <type_traits>
#include <unordered_map>
#include <utility>
 
namespace h5xx {
template <typename T, std::size_t size>
struct is_array<Utils::Vector<T, size>> : std::true_type {};
} // namespace h5xx
 
namespace Writer {
namespace H5md {
 
/**
 * @brief Constants which indicate what to output.
 * To indicate the output of multiple fields, OR the
 * corresponding values.
 */
enum H5MDOutputFields : unsigned int {
  H5MD_OUT_NONE = 0u,
  H5MD_OUT_TYPE = 1u,
  H5MD_OUT_POS = 2u,
  H5MD_OUT_IMG = 4u,
  H5MD_OUT_VEL = 8u,
  H5MD_OUT_FORCE = 16u,
  H5MD_OUT_MASS = 32u,
  H5MD_OUT_CHARGE = 16u,
  H5MD_OUT_BONDS = 128u,
  H5MD_OUT_BOX_L = 256u,
  H5MD_OUT_LE_OFF = 512u,
  H5MD_OUT_LE_DIR = 1024u,
  H5MD_OUT_LE_NORMAL = 2048u,
  H5MD_OUT_ALL = 0b1111111111111111u,
};
 
static std::unordered_map<std::string, H5MDOutputFields> const fields_map = {
    {"all", H5MD_OUT_ALL},
    {"particle.type", H5MD_OUT_TYPE},
    {"particle.position", H5MD_OUT_POS},
    {"particle.image", H5MD_OUT_IMG},
    {"particle.velocity", H5MD_OUT_VEL},
    {"particle.force", H5MD_OUT_FORCE},
    {"particle.bonds", H5MD_OUT_BONDS},
    {"particle.charge", H5MD_OUT_CHARGE},
    {"particle.mass", H5MD_OUT_MASS},
    {"box.length", H5MD_OUT_BOX_L},
    {"lees_edwards.offset", H5MD_OUT_LE_OFF},
    {"lees_edwards.direction", H5MD_OUT_LE_DIR},
    {"lees_edwards.normal", H5MD_OUT_LE_NORMAL},
};
 
inline auto fields_list_to_bitfield(std::vector<std::string> const &fields) {
  unsigned int bitfield = H5MD_OUT_NONE;
  for (auto const &field_name : fields) {
    if (fields_map.count(field_name) == 0) {
      throw std::invalid_argument("Unknown field '" + field_name + "'");
    }
    bitfield |= fields_map.at(field_name);
  }
  return bitfield;
}
 
/**
 * @brief Class for writing H5MD files.
 */
class File {
public:
  /**
   * @brief Constructor.
   * @param file_path Name for the hdf5 file on disk.
   * @param script_path Path to the simulation script.
   * @param output_fields Properties to write to disk.
   * @param mass_unit The unit for mass.
   * @param length_unit The unit for length.
   * @param time_unit The unit for time.
   * @param force_unit The unit for force.
   * @param velocity_unit The unit for velocity.
   * @param charge_unit The unit for charge.
   * @param comm The MPI communicator.
   */
  File(std::string file_path, std::string script_path,
       std::vector<std::string> const &output_fields, std::string mass_unit,
       std::string length_unit, std::string time_unit, std::string force_unit,
       std::string velocity_unit, std::string charge_unit,
       boost::mpi::communicator comm = boost::mpi::communicator())
      : m_script_path(std::move(script_path)),
        m_mass_unit(std::move(mass_unit)),
        m_length_unit(std::move(length_unit)),
        m_time_unit(std::move(time_unit)), m_force_unit(std::move(force_unit)),
        m_velocity_unit(std::move(velocity_unit)),
        m_charge_unit(std::move(charge_unit)), m_comm(std::move(comm)),
        m_fields(fields_list_to_bitfield(output_fields)),
        m_h5md_specification(m_fields) {
    init_file(file_path);
  }
  ~File() = default;
 
  /**
   * @brief Method to perform the renaming of the temporary file from
   * "filename" + ".bak" to "filename".
   */
  void close();
 
  /**
   * @brief Write data to the hdf5 file.
   * @param particles Particle range for which to write data.
   * @param time Simulation time.
   * @param step Simulation step (monotonically increasing).
   * @param geometry The box dimensions.
   */
  void write(const ParticleRange &particles, double time, int step,
             BoxGeometry const &geometry);
 
  /**
   * @brief Retrieve the path to the hdf5 file.
   * @return The path as a string.
   */
  auto file_path() const { return m_h5md_file.name(); }
 
  /**
   * @brief Retrieve the path to the simulation script.
   * @return The path as a string.
   */
  auto const &script_path() const { return m_script_path; }
 
  /**
   * @brief Retrieve the set mass unit.
   * @return The unit as a string.
   */
  auto const &mass_unit() const { return m_mass_unit; }
 
  /**
   * @brief Retrieve the set length unit.
   * @return The unit as a string.
   */
  auto const &length_unit() const { return m_length_unit; }
 
  /**
   * @brief Retrieve the set time unit.
   * @return The unit as a string.
   */
  auto const &time_unit() const { return m_time_unit; }
 
  /**
   * @brief Retrieve the set force unit.
   * @return The unit as a string.
   */
  auto const &force_unit() const { return m_force_unit; }
 
  /**
   * @brief Retrieve the set velocity unit.
   * @return The unit as a string.
   */
  auto const &velocity_unit() const { return m_velocity_unit; }
 
  /**
   * @brief Retrieve the set charge unit.
   * @return The unit as a string.
   */
  auto const &charge_unit() const { return m_charge_unit; }
 
  /**
   * @brief Build the list of valid output fields.
   * @return The list as a vector of strings.
   */
  auto valid_fields() const {
    std::vector<std::string> out = {};
    for (auto const &kv : fields_map) {
      out.push_back(kv.first);
    }
    return out;
  }
 
  /**
   * @brief Method to enforce flushing the buffer to disk.
   */
  void flush();
 
private:
  /**
   * @brief Initialize the File object.
   */
  void init_file(std::string const &file_path);
 
  /**
   * @brief Creates a new H5MD file.
   * @param file_path The filename.
   */
  void create_file(const std::string &file_path);
 
  /**
   * @brief Loads an existing H5MD file.
   * @param file_path The filename.
   */
  void load_file(const std::string &file_path);
 
  /**
   * @brief Create the HDF5 groups according to the H5MD specification.
   */
  void create_groups();
 
  /**
   * @brief Creates the necessary HDF5 datasets according to the H5MD
   * specification.
   */
  void create_datasets();
 
  /**
   * @brief Load datasets of the file.
   */
  void load_datasets();
 
  /**
   * @brief Write the particle bonds (currently only pairs).
   * @param particles Particle range for which to write bonds.
   */
  void write_connectivity(const ParticleRange &particles);
  /**
   * @brief Write the unit attributes.
   */
  void write_units();
  /**
   * @brief Create hard links for the time and step entries of time-dependent
   * datasets.
   */
  void create_hard_links();
 
  std::string m_script_path;
  std::string m_mass_unit;
  std::string m_length_unit;
  std::string m_time_unit;
  std::string m_force_unit;
  std::string m_velocity_unit;
  std::string m_charge_unit;
  boost::mpi::communicator m_comm;
  unsigned int m_fields;
  std::string m_backup_filename;
  boost::filesystem::path m_absolute_script_path;
  h5xx::file m_h5md_file;
  std::unordered_map<std::string, h5xx::dataset> datasets;
  H5MD_Specification m_h5md_specification;
};
 
struct incompatible_h5mdfile : public std::exception {
  const char *what() const noexcept override {
    return "The given .h5 file does not match the specifications in 'fields'.";
  }
};
 
struct left_backupfile : public std::exception {
  const char *what() const noexcept override {
    return "A backup of the .h5 file exists. This usually means that either "
           "you forgot to call the 'close' method or your simulation crashed.";
  }
};
 
} /* namespace H5md */
} /* namespace Writer */
#endif