#
# 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
# 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/>.
#
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 <https://nongnu.org/h5md/modules/units.html>`__.
There are four settable units: 'mass', 'length', 'time', 'charge'.
Units should be written as strings following the specifications defined
`here <https://nongnu.org/h5md/modules/units.html#unit-string>`__,
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:`~espressomd.io.writer.h5md.H5md.valid_fields()` 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")