Source code for pyretis.inout.formats.cross

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

Important classes defined here

CrossFormatter (:py:class:`.CrossFormatter`)
    A class for formatting crossing data from flux simulations.

CrossFile (:py:class:`.CrossFile`)
    A class for handling PyRETIS crossing files.

import logging
from pyretis.inout.formats.formatter import OutputFormatter
from pyretis.inout.fileio import FileIO
logger = logging.getLogger(__name__)  # pylint: disable=invalid-name

__all__ = [

[docs]class CrossFormatter(OutputFormatter): """A class for formatting crossing data from flux simulations. This class handles formatting of crossing data. The format for the crossing file is three columns: 1) The first column is the step number (an integer). 2) The second column is the interface number (an integer). These are numbered from 1 (_NOT_ from 0). 3) The direction we are moving in - `+` for the positive direction or `-` for the negative direction. Internally this is converted to an integer (`+1` or `-1`). """ # Format for crossing files: CROSS_FMT = '{:>10d} {:>4d} {:>3s}'
[docs] def __init__(self): """Initialise the crossing formatter.""" header = {'labels': ['Step', 'Int', 'Dir'], 'width': [10, 4, 3]} super().__init__('CrossFormatter', header=header)
[docs] def format(self, step, data): """Generate output data to be written to a file or screen. This will format the crossing data in a space delimited form. Parameters ---------- step : int This is the current step number. It is only used here for debugging and can possibly be removed. However, it's useful to have here since this gives a common interface for all formatters. data : list of tuples The tuples are crossing with interfaces (if any) on the form `(timestep, interface, direction)` where the direction is '-' or '+'. Yields ------ out : string The line(s) to be written. See Also -------- :py:meth:`.check_crossing` in :py:mod:`pyretis.core.path` calculates the tuple `cross` which is used in this routine. Note ---- We add 1 to the interface number here. This is for compatibility with the old FORTRAN code where the interfaces are numbered 1, 2, ... rather than 0, 1, ... . """ msgtxt = 'Generating crossing data at step: {}'.format(step) logger.debug(msgtxt) for cro in data: if cro: yield self.CROSS_FMT.format(cro[0], cro[1] + 1, cro[2])
[docs] @staticmethod def parse(line): """Parse crossing data. The format is described in :py:meth:`.format`, this method will parse this format for a _single_ row of data. Parameters ---------- line : string A line to parse. Returns ------- out[0] : integer The step number. out[1] : integer The interface number. out[2] : integer The direction, left (-1) or right (1). Note ---- A '1' will be subtracted from the interface in analysis. This is just for backward compatibility with the old FORTRAN code. """ linessplit = line.strip().split() step, inter = int(linessplit[0]), int(linessplit[1]) direction = -1 if linessplit[2] == '-' else 1 return step, inter, direction
[docs]class CrossFile(FileIO): """A class for handling PyRETIS crossing files."""
[docs] def __init__(self, filename, file_mode, backup=True): """Create the cross file with correct formatter.""" super().__init__(filename, file_mode, CrossFormatter(), backup=backup)