Source code for

# Copyright (C) 2010-2022 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 <>.

import sys
import pathlib

from ...script_interface import script_interface_register, ScriptInterfaceHelper  # pylint: disable=import
from ...code_features import assert_features
from ... import utils

[docs]class UnitSystem: """ Data class for writing H5MD trajectories with `physical units <>`__. There are four settable units: 'mass', 'length', 'time', 'charge'. Units should be written as strings following the specifications defined `here <>`__, e.g. ``UnitSystem(time='ps', mass='u', length='nm', charge='e')``. """ def __init__(self, **kwargs): self.mass = '' self.time = '' self.length = '' self.charge = '' for key, value in kwargs.items(): assert hasattr(self, key), f'unknown dimension {key}' setattr(self, key, value or '') if self.length and self.mass and self.time: self.force = f'{self.length} {self.mass} {self.time}-2' else: self.force = '' if self.length and self.time: self.velocity = f'{self.length} {self.time}-1' else: self.velocity = ''
[docs]@script_interface_register class H5md(ScriptInterfaceHelper): """ H5md file object. .. note:: Bonds will be written to the file if they exist. The pypresso script will be written in the metadata. Parameters ---------- file_path : :obj:`str` Path to the trajectory file, or an existing file to append data to (it must have the same specifications). unit_system : :obj:`UnitSystem`, optional Physical units for the data. fields : :obj:`set` or :obj:`str`, optional List of fields to write to the trajectory file. Defaults to ``'all'``. See :meth:`` for the list of valid fields. This list defines the H5MD specifications. If the file in ``file_path`` already exists but has different specifications, an exception is raised. Methods ------- get_params() Get the parameters from the script interface. valid_fields() Get the list of valid fields. write() Call the H5md write method. flush() Call the H5md flush method. close() Close the H5md file. Attributes ---------- file_path: :obj:`str` Path to the trajectory file. script_path: :obj:`str` Path to the pypresso script, or empty string for interactive sessions. fields: :obj:`list` List of fields to write to the trajectory file. mass_unit: :obj:`str` length_unit: :obj:`str` time_unit: :obj:`str` force_unit: :obj:`str` velocity_unit: :obj:`str` charge_unit: :obj:`str` """ _so_name = "ScriptInterface::Writer::H5md" _so_creation_policy = "GLOBAL" _so_bind_methods = ("valid_fields", "write", "flush", "close") def __init__(self, **kwargs): assert_features("H5MD") if "sip" in kwargs: super().__init__(**kwargs) return params = self.default_params() params.update(kwargs) unit_system = params["unit_system"] fields = params["fields"] fields = [fields] if isinstance(fields, str) else list(fields) params["fields"] = fields self.validate_params(params) script_path = "" if sys.argv and sys.argv[0]: script_path = str(pathlib.Path(sys.argv[0]).resolve()) file_path = str(pathlib.Path(params["file_path"]).resolve()) super().__init__( file_path=file_path, script_path=script_path, fields=fields, mass_unit=unit_system.mass, length_unit=unit_system.length, time_unit=unit_system.time, force_unit=unit_system.force, velocity_unit=unit_system.velocity, charge_unit=unit_system.charge )
[docs] def default_params(self): return {"unit_system": UnitSystem(), "fields": "all"}
[docs] def required_keys(self): return {"file_path"}
[docs] def valid_keys(self): return {"file_path", "unit_system", "fields"}
[docs] def validate_params(self, params): """Check validity of given parameters. """ utils.check_type_or_throw_except( params["file_path"], 1, str, "'file_path' should be a string") for item in params["fields"]: utils.check_type_or_throw_except( item, 1, str, "'fields' should be a string or a list of strings")