Source code for

# 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
# 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 <>.
"""Interface module for the H5md core implementation."""

import sys

from six import iteritems

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

[docs]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")
[docs] def get_params(self): """Get the parameters from the scriptinterface.""" return self.h5md_instance.get_params()
[docs] def write(self): """Call the H5md write method.""" self.h5md_instance.call_method("write")
[docs] def flush(self): """Call the H5md flush method.""" self.h5md_instance.call_method("flush")
[docs] def close(self): """Close the H5md file.""" self.h5md_instance.call_method("close")