Source code for espressomd.io.writer.h5md

# Copyright (C) 2010-2018 The ESPResSo project
#
# 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/>.
"""Interface module for the H5md core implementation."""


import sys

from six import iteritems

from ...script_interface import PScriptInterface  # pylint: disable=import


class H5md(object):

    """H5md file object.

    Used for accessing the H5MD core implementation via the
    PScriptInterface.

    .. note::
       Bonds will be written to the file automatically if they exist.

    Parameters
    ----------
    filename : :obj:`str`
               Name of the trajectory file.
    write_pos : :obj:`bool`, optional
                If positions should be written.
    write_vel : :obj:`bool`, optional
                If velocities should be written.
    write_force : :obj:`bool`, optional
                  If forces should be written.
    write_species : :obj:`bool`, optional
                 If types (called 'species' in the H5MD specification) should be written.
    write_mass : :obj:`bool`, optional
                 If masses should be written.
    write_charge : :obj:`bool`, opional
                   If charges should be written.
    write_ordered : :obj:`bool`, optional
                    If particle properties should be ordered according to
                    ids.

    """

    def __init__(self, write_ordered=True, **kwargs):
        self.valid_params = ['filename', "write_ordered"]
        if 'filename' not in kwargs:
            raise ValueError("'filename' parameter missing.")
        self.what = {'write_pos': 1 << 0,
                     'write_vel': 1 << 1,
                     'write_force': 1 << 2,
                     'write_species': 1 << 3,
                     'write_mass': 1 << 4,
                     'write_charge': 1 << 5}
        self.valid_params.append(self.what.keys())
        self.what_bin = 0
        for i, j in iteritems(kwargs):
            if i in self.what.keys():
                if isinstance(j, bool):
                    if j:
                        self.what_bin += self.what[i]
                else:
                    raise ValueError("{} has to be a bool value.".format(i))
            elif i not in self.valid_params:
                raise ValueError(
                    "Unknown parameter {} for H5MD writer.".format(i))

        self.h5md_instance = PScriptInterface(
            "ScriptInterface::Writer::H5mdScript")
        self.h5md_instance.set_params(filename=kwargs['filename'],
                                      what=self.what_bin,
                                      scriptname=sys.argv[0],
                                      write_ordered=write_ordered)
        self.h5md_instance.call_method("init_file")

    def get_params(self):
        """Get the parameters from the scriptinterface."""
        return self.h5md_instance.get_params()

    def write(self):
        """Call the H5md write method."""
        self.h5md_instance.call_method("write")

    def flush(self):
        """Call the H5md flush method."""
        self.h5md_instance.call_method("flush")

    def close(self):
        """Close the H5md file."""
        self.h5md_instance.call_method("close")