Source code for pyretis.inout.formats.order

# -*- coding: utf-8 -*-
# Copyright (c) 2021, PyRETIS Development Team.
# Distributed under the LGPLv2.1+ License. See LICENSE for more info.
"""Module for formatting order parameter data from PyRETIS.

Important classes defined here
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

OrderFormatter (:py:class:`.OrderFormatter`)
    A class for formatting order parameter data.

OrderPathFormatter (:py:class:`.OrderPathFormatter`)
    A class for formatting order parameter data for paths.

OrderFile (:py:class:`.OrderFile`)
    A class for handling PyRETIS order parameter files.

OrderPathFile (:py:class:`.OrderPathFile`)
    A class for handling PyRETIS order parameter files for paths.

"""
import logging
import numpy as np
from pyretis.inout.formats.formatter import OutputFormatter
from pyretis.inout.fileio import FileIO, read_some_lines
logger = logging.getLogger(__name__)  # pylint: disable=invalid-name
logger.addHandler(logging.NullHandler())


__all__ = [
    'OrderFormatter',
    'OrderPathFormatter',
    'OrderFile',
    'OrderPathFile',
]


[docs]class OrderFormatter(OutputFormatter): """A class for formatting order parameter data. The format for the order file is column-based and the columns are: 1) Time. 2) Main order parameter. 3) Collective variable 1 4) Collective variable 2 5) ... """ # Format for order files. Note that we don't know how many parameters # we need to format yet. ORDER_FMT = ['{:>10d}', '{:>12.6f}']
[docs] def __init__(self, name='OrderFormatter'): """Initialise a `OrderFormatter` formatter.""" header = {'labels': ['Time', 'Orderp'], 'width': [10, 12]} super().__init__(name, header=header)
[docs] def format_data(self, step, orderdata): """Format order parameter data. Parameters ---------- step : int This is the current step number. orderdata : list of floats These are the order parameters. Yields ------ out : string The strings to be written. """ towrite = [self.ORDER_FMT[0].format(step)] for orderp in orderdata: towrite.append(self.ORDER_FMT[1].format(orderp)) out = ' '.join(towrite) return out
[docs] def format(self, step, data): """Yield formatted order parameters. See :py:meth:`.format_data`.""" yield self.format_data(step, data)
[docs] def load(self, filename): """Read order parameter data from a file. Since this class defines how the data is formatted it is also convenient to have methods for reading the data defined here. This method will read entire blocks of data from a file into memory. This will be slow for large files and this method could be converted to also yield the individual "rows" of the blocks, rather than the full blocks themselves. Parameters ---------- filename : string The path/file name of the file we want to open. Yields ------ data_dict : dict This is the order parameter data in the file. See Also -------- :py:func:`.read_some_lines`. """ for blocks in read_some_lines(filename, self.parse): data_dict = {'comment': blocks['comment'], 'data': np.array(blocks['data'])} yield data_dict
[docs]class OrderPathFormatter(OrderFormatter): """A class for formatting order parameter data for paths."""
[docs] def __init__(self): """Initialise.""" super().__init__(name='OrderPathFormatter') self.print_header = False
[docs] def format(self, step, data): """Format the order parameter data from a path. Parameters ---------- step : int The cycle number we are creating output for. data : tuple or list Here, data[0] contains a object like :py:class:`.PathBase` which is the path we are creating output for. data[1] contains the status for this path. Yields ------ out : string The strings to be written. """ path, status = data[0], data[1] if not path: # E.g. when null-moves are False. return move = path.generated yield '# Cycle: {}, status: {}, move: {}'.format(step, status, move) yield self.header for i, phasepoint in enumerate(path.phasepoints): yield self.format_data(i, phasepoint.order)
[docs]class OrderFile(FileIO): """A class for handling PyRETIS order parameter files."""
[docs] def __init__(self, filename, file_mode, backup=True): """Create the order file with correct formatter.""" super().__init__(filename, file_mode, OrderFormatter(), backup=backup)
[docs]class OrderPathFile(FileIO): """A class for handling PyRETIS order parameter path files."""
[docs] def __init__(self, filename, file_mode, backup=True): """Create the order path file with correct formatter.""" super().__init__(filename, file_mode, OrderPathFormatter(), backup=backup)