"""
Base classes for the VASP content parsers.
------------------------------------------
Contains the base classes for the VASP content parsers.
"""
# pylint: disable=import-outside-toplevel
from aiida.common import AIIDA_LOGGER as aiidalogger
from aiida.orm import Data # pylint: disable=no-name-in-module
[docs]
class BaseFileParser():
"""
Base class for all the content parsers which parse (read and write) VASP files.
The actually read, interpret and write to/from files is handled by
parsevasp and this interface ensures that the parsing framework in AiiDA and
preparation before submission is successful. The specific content parser
interfaces are always childs of this class.
We assume that there are two main paths when parsing of VASP files takes place.
One is when a file is present and we want to interpret it and convert its
content into one of the usable data structures in AiiDA.
The second is when we already have an AiiDA data structure and want to write a
file based on its content. In the former case we basically
read from a file, while in the latter we write to a file.
The first approach is enabled if we initialize the parser with the argument ``handler``.
This should be a file like handler, i.e. from a context manager telling where the
content can be located. The respective quantities can then be fetched using the
``get_quantity`` function of the instance with the key representing the quantity.
The content of the handler is parsed after
initialization. The valid keys representing fetchable quantities is defined for each
content parser class using the ~`PARSABLE_QUANTITIES~` class parameter.
The second approach is enabled if we initialize with an argument ``data``. This should be
a valid AiiDA data structure node. Using the ``get_quantity('somekey')`` function of the instance
return the same AiiDA data structure node back as was supplied to ``data``.
One can write the parsed content or the content of the StructureData using the
function ``write`` of the class instance.
Parameters
----------
handler : object, optional
A file like object, for instance a file handler representing the file or object
containing content to be parsed. Typically used when parsing completed calculations and is
also the parameter used during initialization of the content parser, when the ``parse``
function of this AiiDA plugin is executed.
data : object. optional
An AiiDA data structure node. Typically used when one later want to write VASP input
files.
settings : dict, optional
Parser settings. Used to set parser settings, e.g. which quantities to compose into nodes etc.
options : dict, optional
Parser options. Used to set extra options to the content parsers. For instance for the
``POSCAR``/``CONTAR`` parser one set ``options.positions_dof`` to supply selective tags to enable proper
construction of selective dynamics ``POSCAR``/``CONTCAR`` from a ``StructureData``. The ``StructureData`` does
not contain this type of possibilities.
"""
OPEN_MODE = 'r'
PARSABLE_QUANTITIES = {}
DEFAULT_SETTINGS = {'quantities_to_parse': []}
def __init__(self, *, handler=None, data=None, settings=None, options=None): # pylint: disable=unused-argument, missing-function-docstring
super().__init__()
# Make sure we only accept initialization with either ``handler`` or ``data``.
if (handler is not None and data is not None) or (handler is None and data is None):
raise TypeError('Supply at bare minimum either argument handler or data to initialize parser.')
# Make sure logger messages in the parser are passed to the AiiDA logger.
self._logger = aiidalogger.getChild(self.__class__.__name__)
# What quantities the specific content parser can provide.
self._parsable_quantities = self.PARSABLE_QUANTITIES
# The container for the parsed data when the ``get_quantity`` is executed, i.e. in the node composer
# at a later stage.
self._parsed_content = {}
# The content parser, which will be an instance of one of the parsevasp parser classes.
self._content_parser = None
# Content data, which is an AiiDA data structure.
self._content_data = None
# Parser settings.
self._set_settings(settings)
# Parser options.
self._options = options
# Set ``handler`` (parsing from some source) or ``data`` (eventually for example executing write)
if handler is not None:
self._init_from_handler(handler)
if data is not None:
# Check that the supplied handler is Data, one of the AiiDA supported data types.
if isinstance(data, Data):
self._init_from_data(data)
else:
raise TypeError('The supplied handler is not of Data type.')
@property
def parsable_quantities(self):
"""Fetch the quantities that this content parser can provide."""
return self._parsable_quantities
def _set_settings(self, settings):
"""Sets the settings to be used for the content parser.
Parameters
----------
settings : None or a dict
The settings to be used for the content parser. Can be None if no settings is supplied
to init. Defaults are then set.
"""
if settings is None:
# Apply defaults
self._settings = self.DEFAULT_SETTINGS
else:
self._settings = settings
if not self._settings.get('quantities_to_parse'):
# Did not find any quantities to parse in the settings, set it to the default
# for each content parser or to an empty list of not defined
self._settings['quantities_to_parse'] = self.DEFAULT_SETTINGS['quantities_to_parse'] \
if self.DEFAULT_SETTINGS.get('quantities_to_parse') else []
# Let us make sure the quantities to parser is in a list form
if not isinstance(self._settings.get('quantities_to_parse'), list):
raise TypeError('The quantities_to_parse is not defined as a list of quantities.')
[docs]
def get_quantity(self, quantity_key):
"""Fetch the required quantity from the content parser.
Either fetch it from an existing AiiDA data structure, a parsed content dictionary
if that exists, otherwise parse this specific quantity using the loaded instance,
which is now a specific content parser.
Parameters
----------
quantity_key : str
A string specifying the key of the quantity to be fetched.
Returns
-------
result : object
If we have initialized the content parser with an AiiDA data structure, we return it in
its original form. If the ``quantity_key`` is not find to be parsable by this content
parser None is returned. Finally, if the content parser was initialized with a file like
object and the requested ``quantity_key`` is found to be parsable we return the quantity.
"""
if self._content_data is not None:
# If we have already set an AiiDA data structure, return it.
# This is straightforward in our case as there is for the PoscarParser,
# KpointsParser a 1:1 mapping between the parser and the AiiDA data (if
# we ignore conversions between representations etc.).
return self._content_data
# We continue assuming we need to parse this quantity
if quantity_key not in self._parsable_quantities:
# Check if this quantity can be parsed by this content parser, if not,
# return None.
return None
if self._parsed_content.get(quantity_key) is None:
# Parsed content does not contain this quantity,
# most likely none of the content is parsed. Parse
# all relevant content now and store.
self._parsed_content = self._parse_content()
return self._parsed_content.get(quantity_key)
[docs]
def write(self, path):
"""
Writes VASP content to file.
Uses the write method defined in this loaded content parser.
Parameters
----------
path : str
A string describing the relative path in the submission folder to write the file.
"""
if self._content_parser is None or self._content_data is None:
# Only write if we have an AiiDA data structure or parser prepared.
if self._content_parser is None:
# If we do not have a parser loaded before write, we have an
# AiiDA data structure. Make sure that is on the form parsevasp expects
# by initializing the content parser instance.
self._content_parser = self._content_data_to_content_parser()
# Now a content parser should be ready and its content can be
# written using parsevasp. But the content parser could still be None
# if there is something with the data that can not be parsed.
with open(path, 'w', encoding='utf8') as handler:
self._content_parser.write(file_handler=handler)
else:
raise ValueError('The content parser has not been initialized or no AiiDA data structure is preparred.')
def _init_from_handler(self, handler):
"""Initialize using a file like object.
Should be overridden in specific content parsers under ``content_parsers``
if it will accept parsable content.
Parameters
----------
handler : object
A file like object that provides the necessary content to be parsed.
"""
raise NotImplementedError(f'{self.__class__.__name__} does not implement a _init_from_handler() method.')
def _init_from_data(self, data):
"""Initialize using an AiiDA data structure.
Should be overridden in specific content parsers under ``content_parsers``
if it will accept an AiiDA data structure. It should also check that the
right structure is supplied.
Parameters
----------
data : object
A valid AiiDA data structure object.
"""
raise NotImplementedError(f'{self.__class__.__name__} does not implement a _init_from_data() method.')
def _content_data_to_content_parser(self):
"""
Convert an AiiDA data structure to a content parser instance relevant for that
data structure. E.g. ``Poscar`` from ``parsevasp`` for an AiiDA ``StructureData``.
Should be overridden in specific content parsers under ``content_parsers``
if it will accept an AiiDA data structure. It should also check that the
right structure is supplied.
Returns
-------
content_parser : object
An instance of a content parser from ``parsevasp``, e.g. ``Poscar``.
"""
raise NotImplementedError(
f'{self.__class__.__name__} does not implement a _content_data_to_content_parser() method.'
)
def _parse_content(self):
"""Parse the quantities configured and parseable from the content."""
quantities_to_parse = self._settings.get('quantities_to_parse')
result = {}
if self._content_parser is None:
# Parsevasp threw an exception, which means content could not be parsed.
for quantity in quantities_to_parse:
if quantity in self._parsable_quantities:
result[quantity] = None
return result
for quantity in quantities_to_parse:
if quantity in self._parsable_quantities:
# In case there is a - in the quantity, we assume we can
# parse this quantity from multiple sources, remove source as we do not want to used
# the source in the property name, i.e. use last element in the split
quantity_splitted = quantity.split('-')
quantity_splitted = quantity_splitted[-1]
result[quantity] = getattr(self, quantity_splitted)
return result